I'm not the author (he'll probably comment here in a sec), but if this is a problem, perhaps this project could become a patch to git itself.

I'd be fine running a patched git that knows about bugs. Of course, then I'd want to make it a little more generic, and not care whether I was dealing with an issue tracker, a wiki, etc.

Bugs are referenced at refs/bugs/<id> and refs/remotes/<remote>/bugs/<id> and those are not garbage collected.

You are wrong about the semantics of git-gc. It will consider for garbage collection all objects that are not referenced, and a reference is everything under refs/*, in addition to the other things you mentioned (index, reflogs etc.).