Yeah, its not always being on good standing that helps because sometimes, you have neighbors that invite them over being heathens. I think the best option for you is just take a few turns out of your busy lifestyle in the game and build as many churches or upgraded churches as you can. That seems to work for me but I am almost always left alone because I care about Religion from turn one, designate just one territory for Priest training and I send them out to the Russians or Moors, ONE A TURN - EVERYTURN. Eventually you get the Theology Guild - DO NOT ACCEPT ANY OTHER GUILD IN THAT FACTION AND IF YOU HAVE ONE DESTROY IT. Eventually you will get lots of Cardinals and then become pope. For me this just works and is worth the effort. I don't know about this game but in MTW the church increases Moral and other traits that you need to squash Squalor and other unrest. It pays to have a church everywhere.