In a perfect world, the nipples would all sit at the same height and the hammer would be a few 1/1000's from touching the nipple when all the way down. Ruger tries to set it's guns up this way...best to check as not all of them are.
For the rest of us, there isn't a good solution. Can either take out the nipples...take out the cylinder...or try the padding of the hammer (basically trying to make it sop just short of hitting the highest nipple).
Padding might give some timing issues...as mentioned, some guns don't release the bolt until the hammer is all the way down. So long as the padding keeps the hammer from hitting the nipples..even if only by .001"..then it won't batter them. Try various thicknesses of padding until you get both, cycling and no-nipple-hits.
Removing the cylinder really messes up the feel of the gun, which is waht dry-fire is all about.
It is possible to break a hammer when it is constantly being beat against the frame...normally, the hammer doesn't hit the frame at all. But if the hammer breaks, you needed a new one anyway.