The Pope doesn't excommunicate you for defending against an invasion. He WILL excommunicate you for relieving a garrison that's holed up in a castle that's being beseiged. If you noticed, when you let the French in, the province turned blue on the map. Everything but the castle was owned by the French that turn. The reason I bring that up is if you're playing to never be excommunicated, you must never lose the land war. Holing up in the castle isn't an option, as the pope will excommunicate you for relieving a siege. I'm not certain how he views if it if just your garrisoned troops sally.