That depends on how bad the threads are.
If they are just bunged up on the major diameter (top of threads) then you could use a thread file to clear them up and then go ever the threads with a thread die. If they are mostly damaged to the full depth of the thread, then your hosed. But not all is lost, you can take the alt. to a re-build shop and have the armature replaced, rather than replacing the entire alt. Look up automotive electric re-builters in your area.