First, sending you that message is clearly a bug. I'll have to look into that at some point.
Second, we've been through this many times before, Chénier. What an auto da fe consists of is a peasant mob descending upon a noble's estate, trying to kill him, and burning the estate to the ground, with servants still inside.
If you don't want to be opposed in your actions by every noble of good conscience, then take actions that don't involve whipping up unruly mobs of peasants against nobility. It's that simple.
It's a noble that instigating the mob. When a lord instigates his faithful to persecute heretics, does the militia or noble-led troops interfere? No, they do not. The game is inconsistent. This is about killing heretics, not about upsetting the social system. Nobody's trying to put peasants in charge. What's the difference between peasants (Troops) replacing a lord via takeover than via a priest action? I don't see units resisting other nobles' units attempting to oust the local nobles.
This is a ridiculously weak action that doesn't even make sense. It could be outright removed and religions would be no weaker for it.
