Well that happened in my English campaign and I ended up ignoring the pope. no one minded,other then the pope of course. And then he sent his Inquisters and same thing happened. I had about 40 family members and about 20 were killed off. So simple, this is what ya do. Train Assasain's and murder them. Worked perfect. Plus Status with the Pope went up. But if they discovered the Assasain, then it is war with the pope and his allies.