Dont Attack Christians

[caravel]

To avoid excommunication pick your targets carefully. Attack, siege and then assault within the two year warning period. Ignore the Pope's warning and expect to be excommunicated. Remember: The Pope will always excommunicate larger factions when they attack smaller ones. So be aware that it may sometimes feel unjust that your aggressor has not been excommunicated but it is probably because he is smaller than you.

If you cannot avoid excommunication, prepare for it. Your provinces will become very unhappy during the excommunicated period, counter this be keeping a good spy and a decent garrison in every province.