You are correct, I think, in that looting temples doesn't cause unrest among the peasantry. Perhaps it should, based on the number of followers. Looting and burning temples should probably cause the same effects as arresting priests. After all, sacking and closing temples using the lord's options does cause unrest. Quite a lot of it.
In a war, the unrest could end up hurting the target realm instead of the attacking realm... It's not entirely unrealistic (Hey! Nobles razed our beloved temples! Off with their heads, all of them!), but it could be unbalancing.
I would see peasant militia being raised, as with non-religious looting, being a better option.
Arresting priests creates trouble for the realm doing the arresting, usually, not the other way around.
