I never seen logical Wynne's position. Probably the Circle broke her. She spent too long time there, her child their taken away from her.
On the other hand: each person is different to tolerate captivity. Someone able to accept the other does not. Same way with the injustice. I know this rage.
They don't all view it as captivity. Some mages actually like the circles, and some mages are given a fair bit of freedom to pursue other interests - like Wynne en route to a meeting in DAA, and Iona out in the forest pursuing her horticulture hobby. Both were circle mages, out and about with permission, not apostates.
I wouldn't say drop Templars all-together, chantry and circles? Maybe, but if there are no circles and mages are free to live their lives as they wish, that also means that, just like regular folks, there will be criminals among them. Templars could be some sort of magic-specific law enforcement ruled by the government of the country - not the Chantry.
Other than that I'd say it's possible to keep the Circles but after big reforms; lower the restrictions and make attendance voluntarily, as well as ruled by mages themselves, seperate from the Chantry and seperate from the government.
Well - I think I might support the notion of dropping templars, because so many of them end up lyrium addicts. The function they perform could perhaps be shifted to mages with dispel magic, mana clash, etc. skills. If mages aren't going to be confined to circles, you'd probably want some of these magic-fighting mages in the ranks of your local law enforcement organizations - and these mages would be provided with a supply of lyrium as needed.
I'd require newly identified mages to attend a circle (as a boarding school) until they could pass a skills test demonstrating they have enough control to avoid magical accidents that may harm persons or property (including themselves). Once they'd passed the tests, they would be allowed to go, or stay for more advanced training. They'd be allowed to exchange letters and have visitors while there.
I'd create an independent Seeker order, perhaps similar to the Grey Wardens as the last line of defense against mage criminals / magical corruption, etc. They might maintain phylacteries, just in case. They might also be the authority responsible to manage the lyrium trade.
I'd keep blood magic or training in blood magic completely illegal, and restrict lyrium to those mages working in law enforcement.
I might also conscript these free mages to local militias to be available to deal with demon / abomination problems on a local level as they arise. The price of freedom and all that.
Shrug.