The pope was never a fair man. He isn't excommunicating leaders out sense of justice. It's a diplomatic weapon. He's clearly allied with the French and uses the threat of excommunication to ward off any who would oppose the French.

See if the pope is getting old. If he is, use the opportunity to make gains from the French, take the excommunication and wait for the pope to die.

If it's justice you seek, then don't play MTW.