I don’t think that was fully worked out, and the whole thing was not put through peer review but was only published on the day of launch. I think that if the astronauts had become sick, they would have been removed from the quarantine facilities immediately. It’s hard to see how they could do anything else ethically unless they had clear evidence that they were indeed sick due to the presence of extra terrestrial life.
They decided to remove the crew from the command module using divers in a dinghy, then airlifted out using a helicopter, just because the machinery wasn’t functioning properly to lift the module out using a crane as originally planned. The main risk there was that the astronauts could have got seasick as they waited for the crane to get sorted out. That was an immediate breach of quarantine as some of the lunar dust must surely have got into the sea at that point. So, given that they broke the quarantine so easily for relatively trivial reasons, they would surely have taken them out of quarantine if they had truly got sick.
It was just a token guesture anyway at that point as they had already exposed the ocean to lunar dust at that point.
Gene Cernan covered in dust in the lunar module after his moon walk. See The Mysterious Smell of Moondust. It got everywhere and smelt like gunpowder (curiously, nobody knows why to this day). This is from a much later mission, and they were no longer being quarantined - I’m just sharing this because it is a good image of an Apollo astronaut covered with lunar dust.
Some of this very fine dust surely got into the ocean when they opened the command module door for Apollo 11 - and after that the rest of the quarantine procedures were mainly token guestures.
As C Stuart Hardwick, says in his answer, they didn’t know about extremophiles and they also didn’t know about ultra microbacteria or the research that shows that extra terrestrial life could be even smaller, way beyond optical resolution. They just didn’t know enough microbiology or have enough science to do the job adequately. But also, how could quarantine work anyway against unknown microbes? It gives no protection from microbes that have a latency period longer than the quarantine period, or ones that are harmless to humans but harm our ecosystems.
One example I like there is, what if they had returned a photosynthetic lifeform that was more efficient than any Earth based photosynthesis? We have several different forms of photosynthesis on Earth including the red haloarchaea that turn the red sea red, which work in a similar way to our eyes, not producing oxygen at all. So there may be other forms of photosynthesis we don’t have on Earth and what if some lifeform got returned to Earth which is more effective at photosynthesis than any Earth lifeform, and got into the sea and replaced the green algae which are the basis of many of the foodchains in the oceans and also produce much of the oxygen we breathe? What if they produce some other gas, which is harmful to us, or are inedible to sea creatures, or produce toxins that make sea food harmful to us? Something like that would show up no problems at all in quarantine probably. It might even need to evolve a bit before it can become prolific in the Earth’s oceans.
Or what if it is just an all round more efficient metabolism and (perhaps after a period of proliferation and adaptation) replaces microbial Earth life in almost all niches? But again is toxic to us or just doesn’t produce the organics we need for food?
So, I think there is too much emphasis on quarantine even today as a way to protect Earth from extraterrestrial life. It would do almost nothing to protect against an unknown hazard. It’s only effective when you know what it is that you are quarantining against and why you are doing it, and what the latency period is before symptoms manifest and you know that it is a hazard for humans, rather than any other lifeforms on our planet.
As for the 1960s procedures they are more interesting today as valuable lessons about what can go wrong when you try to do planetary protection. And we were just lucky. If there had been any microbes on the Moon hazardous to the environment of Earth the measures we took wouldn’t have done much to protect Earth. By then they already thought the chance of life there was very low. They knew that the Moon had no significant atmosphere and no liquid water on the surface, though there was still a possibility of life in moist layers some tens of meters below the surface and possibility of dormant life on the surface.
With billions of people potentially affected, you have to take precautions even if the chance of anything happening is tiny. They did token guestures of planetary protection, which showed that they had given it some thought and cared about it, but they didn’t actually do much materially to protect Earth.
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