Choosing to destroy the chantry would be such a waste of a very useful potential political tool, My Characters would like to save it but implement major reforms within the chantry while also placing them under his thumb =D
Also the persuit of the genocide of Templars and or Mages is also a complete waste of a useful political tool, its also completely ****ing insane.
The way I see it, Kirkwall was a ticking time bomb. The Veil was thin there, so demons were more likely to cross over and possess mages/mages would be more likely to turn to blood magic. Anders has always hated the Chantry, and then Hawke comes along and finds the idol, which Bartrand ends up giving to Meredith. Then the Viscount dies and a soon-to-be insane Meredith takes over. With Meredith now insane, things become even harsher than before, and Anders becomes even more outraged, which leads him to blow up the Chantry.
Some Circles are particularly strict, while others are less so. Mages see it differently. There are different parties of mages, after all.
- Aequetarians: largest fraternity, especially in Ferelden; believe mages should help people regardless of Chantry law; they believe they should cooperate with the Chantry by complying to its more reasonable laws
- Isolationists: small fraternity; believe mages should separate themselves from everyone altogether
- Liberationists: pro-Circle, but believe it should not be run by the Chantry
- Loyalists (or "Chantry apologists"): believe that mages should follow the Chantry's laws completely, including constantly being watched by the templars
- Lucrosians: priority is to accumulate money, and gaining political influence a close second
So Aquetarians believe magic should be used for good and that the Chantry should continue to oversee the Circle, though that they should be less severe.
Isolationists are anti-Circle.
Liberationists are anti-Chantry-run Circle.
Lucrosians... well, who cares.
I'm sure after Anders made the Chantry go boom opinions started to change. I can't recall Asunder perfectly, but it sounded like, after the events of Kirkwall, Liberationists became much more prominent.
So the Chantry isn't necessarily key to the Circle, though it's impact is obviously significant.