so long as you cook the garlic the heat should kill any spores if indeed there were any on your garlic.

Seems like a question for the Harvest Forum. It's the canning/preserving forum here and they regularly deal with food safety so they'd know for sure. Your garlic is probably fine.

Rodney

I agree with Rodney about the Harvest Forum. There are people there who would know exactly why it would be safe or not and how you could/should use it.

I realize this is a rather late response but..

What do you mean the outside sheathes were rotting? As in slimy gunk, or mold, or black speckling, or white fibrous stuff or what? Garlic can get some different rotting going on.

And the outside was rotting but the cloves were fine? As in just the few outermost layers that surrounded the whole head were funky, but once you opened the head up the insides were fine? Kind of like how an onion can have funk on the outer layer but the whole interior can be fine?