Couldn't finish off everyone of faith. He would have to know where everyone was to be able to kill all of them. I hope you just misread what I wrote...
To start with, he could have steam-rolled (as in, kill every living soul, in totality) present religious troublemakers like those in Albania and Chechnya, and have no one bother him with questions or opposition. Why did he not choose that option? Because they were not a political threat to him.