Yeah, the papal reemergences I try to avoid, but when you get excommed and don't have high level assasins around, it's tough luck, though keeping the provinces open and letting rebels take over for the papacy to start when they reemerge is a good idea.

I find that the loyalty level and spies in the province doesn't always prevent a faction's reemergence. The Swiss came back 3 times in my last Byz campaign on Expert