Game engine trumps roleplay.
Killjoy trumps people trying to have fun in a way he disagrees with, evidently.
Temples were destroyed, threats were made. As I said, it could still be worse. However, it'd be a total and blatant lie to claim that no damage whatsoever was done against the church. It's not because Aurvandil could do worse that it hasn't done anything wrong at all.
You admit it yourself. "Save for one temple". That's already one temple too much. The Church hasn't counter-attacked because it doesn't want an all-out conflict, but that's a long way from feeling like it has been properly treated by your atheist government.
No threats were ever given as far as I am aware, and if they were they certainly were not made by anyone with the support of Aurvandil in doing so. The temple that was destroyed was done by a rogue lord who was soon removed from power.
The Elementalists already stole a duchy, discussed waging a religious war on Aurvandil (I saw the letters where they speculated on launching a first strike on Aurvandil) and tried to enact religious oppression in Aurvandil by trying to force their religion on lords and regions that did not want it. You are right, it could have been worse, the Elementalists could have actually been persecuted like you say they were.
Also, Aurvandil's government isn't atheist by any measure.