Oh, I know very well. Religion could easily be used to do all sorts of damage.
(Though it's not quite as easy as you think - you can't takeover regions which have high realm control)
But the problem is that this is a qausi-religious war. As in the cause of it is mostly religious and there are lots of Arcaeans intolerant to Sartanism but it's not yet at the point where it's a case of Sartanism versus Arcaea. If it was then things would be different but as it is there's no enthusiasm for the entire religion picking a battle with Arcaea in case it loses.
The only way religious takeovers will happen is if Arcaea makes this a religious conflict - the elders of the church don't want to escalate things.