Quite honestly, I'm inclined to disagree, if mostly for theme and flavor reasons. If a city has been inhabited by demon-worshipping heathens for any substantial time, I would imagine the only way to be
sure that you have removed the foul taint of the hellspawn would be to put the city to the torch, tear down the charred remains and then sprinkle holy water over the blackened earth remaining. And then
maybe. "Just" converting the population with sword and fire just won't cut it when dealing with the taint of Hell that the followers of the Ashen Veil would have allowed into the world.
Besides, it makes the battle against Armageddon much more brutal and fierce. You can't just capture a city and then inquisition it and then go on, if you want that Counter to go down you have to be ruthless, which again fits the theme perfectly. If you want to avert the end of the world, sacrifices will have to be made.