Quote Originally Posted by Lemur
Oooh, wait, I know how to handle this one. If you've got a high-level assassin, just take out the Pope and the excommunication is over. Or you can send a diplomat and keep donating 1000 florins until your relationship is Very Good or better, at which point you can request an end to the papal ban.

The death of your faction leader will also fix things, but that's kind of not what we're looking for.
Belive or not, I just tried this about 5 mins ago...I got pwned.