I don't have AC in it so I don't know how crammed it is in there, but can't you replace diodes and/or brushes while it is still in there? So without removing it?
Anyway, I don't think batteries can damage an alternator. It is only possible to damage batteries with a bad alternator (broken regulator giving a very high voltage for example)
In this case, if you are certain that your alternator is broken, it is probably because it is old. And you may think your batteries are dodgy because they were not charged properly by your alternator.