You could only declare as many nobles anathema as you have priests.
And if you have soldiers, you'd be less likely to get mobbed in the first place.
But frankly, if a realm with an army of, say, 5 nobles and little money to buy reasonably sized units decides to attack an empire with the political support of a religion with 5 priests (which is, like, a half-dozen of the biggest religions in the game, AFAIK), then they're going to be ROTFL-stomped one way or another.
But to prevent that abuse, we could also make a cooldown: a religion can only add another declaration of anathema every 2 weeks or something. So it would take the religion at least 10 weeks to declare against that whole realm.
But frankly, I don't see this as a big problem. This would require a religion to have no conflicts prior to the war, a relatively vast number of priests, very weak units among invaders....
The only time I would see it having strategic import would be if the invaders struck deep into enemy territory, then were defeated in battle, and had to retreat through territory with high anathematizing religion follower counts. With weaker units, they would have a chance of getting mobbed.
Hmmm... defeated heathens retreating through the lands of the faithful have a chance of facing popular religious violence. Oh, that sounds exactly like what would happen in the Middle Ages.
