The rules for excomunication is quite simple. If a faction with twice the number of regions attacks, he gets a warning. Any aggressive action before the warning runs out leads to excomunication. Sally out of a besieged castle is not aggressive (since the patch) but retaking lost a region does count as aggressive. Attacking the papist is automatic excomunication. Blocking a crusade in conquest mode is automatic excomunication, in glorious goals mode it depends on if the crusade's object is a goal or not.

Being friendly with the pope has no effect on the rules. But he will send you cash if he has any spare.