You have no choice but to cut out the offending joist and double-header it (creating a box in which to drop the closet bend). The only other option is to reposition the toilet. You should use plenty of metal re-inforcements, such as Simpson Strong-Tie connectors. This seems like a situation where the carpentry contractor screwed up, and I’d suggest doing what I do in such situations…vent your frustration by cussing them out, and go ahead and do what it takes to get the plumbing properly in place.
NtP