If we take them as if this were a society that should function as a real society would, and people who act as real people would; The religious issue would be secondary. All societies, especially theocracies, are pragmatic about their faith in government. When the fake inquisitor was kicking around some country bumpkins were easily awed and terrified into doing what ever; but now we're talking about the central governing body of the capital. That said; an alternative would have been to have your Patron throw your compatriots on the mercy of the court. After all; the charge was no actually heracy, and the court, aware of the scions actions and the politics of executing them, would have been disinclined to do so. It could have driven the player to learn more about the Ishgard conflict; by having the court enforce a kind of conversion.