Each Circle would be independent of other Circles, and would be vassals of the crown. The Circles would have an establishing charter and their members, mage and templar alike, would have to take an oath. Violations of that oath, including any attempt to rule beyond the bounds of the charter, would be cause for other members of the circle to stop the transgressor, including trial and punishment. If the Circle itself were trying to establish a magocracy, then other Circles would be obliged to defend the kingdom from the threat. If all the mages of all the circles decided to take over, well... much like under the corrupt Andrastean system, there wouldn't be much anyone could do to stop the mages if they somehow all miraculously decided to work together for a common purpose.
I wouldn't handle someone like Anders. A Circle I created would be entirely voluntary, so Anders would either join of his own free will or not be in it. Not hunted. No Templars trying to lure him into a stupid, stupid trap. Of course, if Anders chose not to be part of the Circle, he would not have the Circle's protection, so whatever he did would be subject to the common law. If he were determined to be a danger to the kingdom, the Circles would be obligated to defend the kingdom from that threat.
It might come to pass that mages and templars hunted down Anders and killed him, but it would be in accordance with secular law as a result of crimes committed by Anders, not because Anders was an apostate and simply chose to exist outside of the circle system. If he just wanted to run a free clinic, he would be free to do so.
Edit: Also, while a Circle mage would be prohibited by oath from rule beyond the grant in the Circle's charter, there would be nothing to keep a non-circle mage from inheriting a title, receiving a title from the crown for service therunto, etc. That title would be held by the mage as an individual, and passed to heirs under its own terms (e.g. primogeniture, in accordance with the customs of the kingdom.)