The Popeness attacked me, in my current Venice campaign, and I was thusly excommed for the entire game. I finally decided to try and get reconciled with about 30 turns to go, and it cost me 100,000 florins, plus six territories. Yes, the Pope really disliked me. :0

In all of my other Catholic games, I do as others have mentioned and give him handj...well, pay him a lot and keep him happy. That way I never have to deal with reconciliation. This Venice camp is actually the only one I've been excommed in, I think, outside of the original MTW.