Without hurting him you have to wait until your king or the pope dies. Of course to end a excommunication by means of violence, like mentioned there are three ways, by assassination, inquisition, and faction elimination.
A lot of people bypass the pope by attacking one enemy that they don't really want to take over, getting a warning and retracting, and then attacking a second enemy, the true target. This works because the pope will only keep track of one warning at a time. After a warning you have ten turns to campaign somewhere else. If you play it smart and keep track of your warnings, you can conquor and never get excommunicated. I'm not sure if they pope will still excommunicate you if you are defending yourself though.
The pope will for sure excommunivate you if you are sieging an enemy catholic but I am not sure about whether he will if you've cleared the province of enemies. The pope may or may not still consider that province as belonging to you enemies.
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