Well, if the Pope attacks you militarily and you simply repel him do you get ex-communicated ? I would wager not but I'm just preparing myself as I've conquered the Italians and Sicilians and I've surrounded him and he has no fleet to harass me with.

I know that if you eliminate him he returns with stacks of the best troops which I'd rather not have to face so I wouldn't mind him staying in his face and periodically getting b***h slapped by my defensive border armies.