What I do to stop the pope problem:

Play As A Pagan, Orthodox or Muslim Faction! :)

Or

I am not really bothered about being excommunicated since nothing usually happens (except the rebelions - which i stop by lowering taxes to High and have a few more men in a province), if i get the message "withdraw your troups" if i finish the job fast i dont get excommunicated (you gotta love mercs). When im going for 100% i make sure i dont attack the pope, i keep em alive because they reapear like cockroaches and then when there is only us left, i kill em and "poof" 100%.