I have found that sometimes it is better to ignore excommunication. The unrest caused is bearable in comparison to having to endure a grave military threat. Even with the diplomatic improvements of the leaked 1.2 the ai is configured to be hostile towards the most successful factions. Each and every faction will need to be humbled militarily regardless. Relations with the Papacy, particularly one without land can be restored fairly quickly if I can afford to donate provinces to the Church. Usually the conventional strategy of creating as many priests and churches as possible, evangelising when the risk of heresy is low, and giving spiritual gifts to the Holy Father is what I follow. Yet sometimes that just isn't possible.