Well at the time of the lunar landings, they already knew that the Moon had negligible atmosphere and as a result, they knew there was no standing water or running water on the surface. It just couldn’t survive for more than minutes in those conditions (depending on its thickness) based on well understood physics.

However they couldn’t rule out life completely. Our knowledge of the Moon was very limited and they thought that there was a possibility that life evolved on the early Moon and had survived through to the present a few tens of meters below the surface, where, they thought, there might be some moisture.

Indeed the earliest lunar probes to the Moon were sterilized to avoid contaminating any potential habitats below the surface. See Carl Sagan’s very early paper on this topic: Biological contamination of the Moon (November 16th, 1959 written soon after Luna 2 - the first successful impact on the Moon by a Russian spacecraft). By the time the Apollo astronauts went to the Moon, I think most would have said the chance of life there was tiny, but still, there was enough of a possibility that there was general agreement that they needed to take some protection measures.

However the actual quarantine precautions they took were more of a token measure, to show that they cared, and didn’t actually protect Earth at all, really. I watched at the time (via television) and like just about everyone else, I had no idea that anything was amiss. But Carl Sagan (who was an expert in astrobiology, many don’t realize this) was dismayed to see how they took the astronauts from the lunar module to the waiting ship. They just opened the door of the lunar module as it bobbed around on the ocean, passed in the decontamination suits, the astronauts then put them on and tumbled into the dinghy and then were airlifted out by helicopter. Their original plan was to lift the entire module onto the ship using a crane but there was something wrong with the crane, so rather than keep the astronauts bobbing about in their command module and probably getting seasick while they fixed it, they opened the command module in the open sea and used this approach instead.

The astronauts remarked on how the very fine dust got everywhere, inside their spacecraft.

Gene Cernan covered in dust in the lunar module after his moon walk. See The Mysterious Smell of Moondust

They could smell the fine dust (smelt and tasted like gunpowder) which was floating in the air of the cabin. (Nobody quite knows why it smells like gunpowder as it doesn’t contain any substance resembling gunpowder).

Definitely some lunar dust ended up in the ocean at that point. So, if there had been any life in the lunar dust, it would have ended up in the ocean, the worst possible place to contaminate with extraterrestrial life, right then and there. After that, the quarantine was really just a token measure.

There were several other breaches of quarantine, and these quarantine attempts from the 1960s are now regarded as more important for their historical value, for what it teaches us about how not to protect Earth and what can go wrong, rather than as examples of how to do it. In any case, we now know of microbes such as the ultramicrobacteria far smaller than anything they knew about then, and from works on limitations of size, experts think that extra terrestrial microbes could potentially be even smaller, perhaps of the order of tens of nanometers in diameter, which makes them far too small to see with an optical microscope (with diffraction limited optical resolution of 200 nm). We could only see them with an electron microscope or similar. We also know of extremophiles with capabilities to survive vacuum, heat, cold, acid, ionizing radiation, and many other conditions, which they didn’t know about back then. So in the 1960s, even if the precautions had been peer reviewed and they’d got all their best scientists to work on the best possible way to do it, they just didn’t know enough microbiology back then to design adequate precautions to protect Earth .

Also, the quarantine facility wasn’t that well sealed. Buzz Aldrin says in his “No Dream is Too High” (page 150) about their time in quarantine:

“The unit was comfortable, but there was little to do and nowhere to go, so we got bored in a hurry.

One day, I was sitting at the table staring at the floor, and I noticed a small crack in the middle of the floor, with tiny ants coming up through it! Hmm, I guess this thing isn’t really tightly sealed, I thought. Imagine, if we had brought some sort of alien substance back with us, those ants could have contracted it and taken it back out to the world!”

Also, the three weeks quarantine was not established through peer review either. The quarantine regulations were published on the day that Apollo 11 launched to the Moon which didn’t give anyone else any possibility to review and change them. This would not be permitted nowadays.

Actually latency periods can be of the order of decades for some diseases, as Carl Sagan pointed out, taking the example of leprosy. Even rabies now has a quarantine period of several months.

As well as that, if the astronauts had become seriously ill in quarantine - well I think you can be reasonably confident that they’d have been taken out right away and into a good hospital to treat them. After all the mission planners breached quarantine just to get them into the ship quickly instead of waiting until the crane was fixed. If they thought it was that important to avoid astronauts experiencing the discomfort of seasickness, then surely they would have taken them out of quarantine into hospital immediately if there was any sign that their lives might actually be in danger.

It’s also not at all clear that you can ethically keep someone in quarantine when you don’t know for sure if there is a risk to everyone else and when their life is in danger. Even if they volunteer to do so themselves, and sign some agreement or whatever, to say that they volunteer to stay there no matter what - if they then were dying and you could save their lives by taking them out of quarantine into hospital, how could you leave them in quarantine, unless you had clear and certain evidence that it was a hazard to everyone else to take them out? I don’t see how you can.

Then, there’s much more to quarantine against, not just microbes that could somehow impact on humans. Anything that could impact on the algae in the sea, or plants, or animals, would also need to be contained. A symptomless human quarantine would not guarantee that the microbes are safe for all Earth life.

So - it’s hard to see actually what they could have done by way of effective protection of Earth with the technology they had at the time, except just not send humans to the Moon. We are just lucky that the Moon had no lifeforms of any sort (as far as we know) and the returned lunar dust and rocks are of no danger to Earth. I can imagine that other extra terrestrials in similar situations might visit a nearby moon or planet and bring back lifeforms that make them extinct, or damages their ecosystem. There’s nothing biologically implausible about that, as the Nobel prize winning microbiologist Joshua Lederberg was perhaps the first to make clear.

I think actually that there is still a very remote chance of liquid water deep underground on the Moon - that’s because of new research that suggests that it wasn’t entirely dry when it formed, combined with indirect evidence of volatiles escaping from the interior and freshly surfaced small regions that could be due to gases released from deep underground. The center of the Moon is still very hot, and if there are indeed volatiles below the surface, from a lower “wetter” layer of rock that condensed first, perhaps there could also be liquid water at some depth. Some think there could be ice below much of the surface of the Moon at a depth of some meters. That’s a minority view, but we don’t yet know enough to rule this out.

However the lunar surface is thought of as totally sterile, and for purposes of planetary protection is classified as category II meaning you don’t have to take any special precautions for rovers or human visits, just document clearly what you do and any crashes too, so that others can take account of any contamination you may introduce when analyzing lunar samples etc.

So, there’s no need to take any special precautions for sample returns from the Moon and no planetary protection issues for Earth or the Moon with sending astronauts there - that’s the scientific consensus of many experts. But there is for samples returned from further afield. The lunar quarantine regulations have been rescinded and anyway would not be considered adequate nowadays, even if they had been applied exactly as specified, so something new is needed.

The most recent ESF study on how to deal with samples returned to Earth from Mars recommends returning them to a new type of facility which has to contain them right down to the level of GTAs as well as the smallest size of microbe they think is possible using unknown extra terrestrial biology. Their recommendations are that it has to be capable of containing particles well below the optical resolution limit of 200 nanometers (ideally it shouldn't permit release of particles over 10 nanometers in diameter and shouldn’t permit release of 50 nm particles under any circumstances).

In other words, the facility has to be able to contain particles only visible with electron microscopes or similar. This is well beyond the capabilities of a normal biohazard level 4 containment facility where the aim is to contain known hazards of known size and capabilities. The problem is that it has to be able to contain any conceivable extraterrestrial biology. That’s particularly hard to ensure when we don’t have any examples yet of any extraterrestrial biology at all. So how can we be sure that the facility will contain it? Only by building a very expensive facility that protects against all conceivable possibilities, even the most unexpected.

It also has to protect the samples against contamination by Earth life, even by a few amino acids.

Also, there's all the extra legislation to pass. Margaret Race looked at it. You'd be astonished, there are many domestic and international laws, needing to be passed - which were not needed for Apollo because the world nowadays is legally far more complex. After reading her paper, I think it could easily take well over a decade just passing all the laws even if everyone agrees and there are no objections, and surely longer if there are objections.

I think myself that by far the simplest and also safest solution is to either

1. Sterilize all samples returned to Earth - you can do that in such a way that you preserve biosignatures to help study them for traces of life, or
2. Don’t return them to Earth, instead return to an orbit above geostationary orbit. Do preliminary investigation there in robotic facilities controlled from Earth. Any equipment is only transferred one way, from Earth to orbit, and any material that goes the other way is sterilized unless we have studied it sufficiently that we are confident that there is no life in it, or that any life is safe for Earth.

Our first sample returns from Mars or Europa are not likely to happen until the late 2020s, and by then we will surely have easy ways to send hundreds of tons to GEO. Indeed, my suggestion is just a modification of one suggestion of a way to return samples to Earth - that you send a spaceship up to rendezvous with the return capsule and return it to Earth. I’d go along with that as far as retrieving the sample in a spacecraft launched from Earth to meet it - but after that, I think it is far simpler to just keep that spacecraft above GEO while we examine the sample more closely. Perhaps a few thousand kilometers above it, far enough so that there is no chance of cross contamination with any operations going on in GEO. Then send instruments up to it from Earth and study it there. Almost anything can go that way, except for investigations using giant particle accelerators, and for those, you can sterilize any samples returned to Earth.

Then either you find out quickly that the samples are harmless, or this becomes the basis of a telerobotic facility to study extra terrestrial life in orbit. That way you don’t have to build the half billion dollar receiving facility on Earth - which might turn out to be entirely unnecessary - and you don’t have to spend a decade or two passing new laws to permit the sample return (which again might be unnecessary laws if the material is harmless and requires no precautions as happened with the Moon) as all of this can be done within the existing legislation. And it’s also safer for Earth, you don’t take even the slightest of risks (you can return to above GEO using trajectory biased orbits that never intersect with Earth). With a facility on Earth, even if perfectly designed to contain the material at the nanoscale level, even if you are correct that the building will contain all concievable forms of exobiology, there’s the chance of terrorist action, natural disasters, even crash of the helicopter or train transporting samples to the facility, negligence or human error by its operators, etc etc.

In my view, it’s just simpler all round to keep the samples in orbit above GEO. And don’t send astronauts there until you know what is there and that it is safe for them. If it is harmless, you find out first, and if not, it’s a case of a known hazard by then, you can then make properly informed decisions about whether it is safe to return to Earth and what precautions are needed, or whether you need to continue to study it in orbit.

As an example of a discovery that would prove that the sample is harmless to Earth life - if it consists of autopoetic cells or some precursor for life, you might decide quickly that it is no match for Earth life which would just eat it up. While in the other direction, if it was some exotic form of informational polymer, perhaps TNA, or PNA, a more robust form of DNA, or more compact cells, better at photosynthesis or whatever, you might decide that considerable caution is needed before returning it anywhere near Earth itself, and it might continue to be safest to just study it in robotic facilities above GEO.

LEO is no good here, as anything in LEO will eventually fall back to Earth as it is still in the Earth’s atmosphere. Above GEO is the ideal location as it is as far as you can get from either the Earth or the Moon in terms of delta v with over 1 km / sec needed to get to a geo transfer orbit to hit Earth and a similar amount of delta v needed before it can hit the Moon. While satellites in GEO itself or in the graveyard orbit a few hundred kilomters above it have very small relative velocities and even if you get a runaway chain reaction of the satellites destroying each other through the Kessler syndrome, the debris won’t go far, so your facility a few thousand kilometers above GEO will still be safe.

See also Why quarantine won't work - protecting Earth, and humans sent to Mars, from Mars life (if it exists) in my “Case for Moon First”.