Dude, you killed three thousand peasants, and like Delvin said, booted a Lord out of his Lordship, which is the only way shy of banning to do so in the game. There are correct ways to use this mechanic. its not a "push button to win" mechanic. I can think of at least four different scenarios just off of the top of my head.
Furthermore, nobody should be forced to ally with you. Yea, I'm a follower of religion XYZ, and a priest of XYZ just booted my Duke out of his lordship because he was recently excommunicated. However, my loyalties lie with my Duke as opposed to my religion at present. I'm going to side with him. Or, it could be reversed. However, I agree with Delvin's assessment:
Whipping up mobs of peasants to depose the rightful lord should bring down the scorn of every noble. You're causing a riot. It is natural to put down riots, as opposed to join in. When a lord persecutes followers of his religion, it is an organized action. Troops are involved, and they carry the weight of the law around with them. Some random foreign noble peddling a religion does not carry that authority.
For historical reference see: every dispute between the catholic church and secular rulers ever.
