They'll probably end up forming new nationalized circles under state authority, given that it makes the whole logistics thing easier to handle and keeps potentially dangerous mages confined in one easy to control place.
If they haven't done so by Trespasser, I doubt they're going to do so, especially now that the College and Circle are competing with each other. Trying to force nationalization would just cause another war, and I wouldn't be surprised if Vivienne's political influence is keeping people from doing that.
That's right, why would they hire someone who would actually have a chance to fight them if they go rampaging, right? Let's exile/ignore/discredit/whatever everyone with ability to nullify magic and hire sellswords who are good only for scaring non-mages!
Hey, it's hardly my fault that almost every templar decided to join Corypheus, and anyone left decided to quit lyrium when they saw Cullen's example. Now, if only there was a nation, preferably one that's stood for thousands of years, that's never used lyrium-addicted templars and yet has never fallen to rampaging abominations... hmmm...