They would retreat to the Soyuz TMA. The ISS usually has two of them attached to the ISS as safety measure "lifeboats" (as many as are needed for the crew, three per Soyuz so a 6 person crew needs two of them). They could fly back to Earth at last resort if they can't repair it.
The ISS has shielding for smaller micrometeorites up to a mm or so across, they use "whipple shields" - a multi-layer approach with gaps between the layers to slow it down and then stop it. First layer is just a thin layer of aluminium but it is enough to break up the meteorite, melt or vaporize it and second layer then catches the slowed down debris.
The Cupola has four layers of glass. If any of them is damaged it has an extra shield on the inside that goes over that pane for extra protection on the inside, which is only removed again once NASA has assessed to see if it is safe.
Larger meteorites are very rare.
Here is a meteor strike that chipped a bit out of the outermost pane of the Cupola.
If the ISS does get seriously damaged, they then would have the difficult decision to make, whether to de-orbit it immediately, or whether to boost it to a higher orbit for possible repair. They would aim to make that decision within 14 days of the emergency.