Quote Originally Posted by Darth Revan
Send assassins until the guy loses it assassination is the best way of getting rid of the pesky pope
I've discovered that a nice alternative is to burn him at the stake with a Grand Iniquisitor. The GI won't die if he fails, plus I find the thought of the Pope being convicted of heresy deliciously ironic.

Otherwise Mystic, I would recommend taking Agent Miles' advice. Pick one Catholic faction to attack to draw the Pope's warning, and then you're free to war with the other Catholic factions for the next decade without worry. I know some MTW players find said tactic to be an exploit--and in all fairness they would be correct--but I personally am quite okay with that, given how unbalanced/unfair the Pope often is in regards to excommunications.