Wow. This is an ...interesting thread! Lemme just throw this argument in here:
The Circle approach is, at its heart, reasonable. Its failure, however, was inevitable.
Mages are born with power that nonmages can not match. This is just fact.
As a direct result of this state of birth, mages are also at greater risk of Going Darkside - turning to blood magic or turning into abominations. This is also fact; partly because of the way demons work, partly because that's also the way people work. (see: all of human history with regard to the accrual of power.)
The Circle is, at its core, *not a bad idea* - you take someone who can be tempted to go darkside and you remove the temptations, as much as you can. You give them food, shelter, safety, peace. As much as you can. And you set people to guard them so that people can't put them in fear, which is itself a temptation to reach for power. And you say "here is the line" - blood magic usually being the line - and let them be.
Origins shows that this mostly did, in fact, *work*. Most mages, given safety and peace, and Irving's willingness to let mages leave the Tower on this or that mission if they could act like responsible adults, resulted in peace. It's reasonable, as well, to say that in Ferelden at least, the Circles were willing to overlook those mages who preferred to live free, provided they didn't draw attention to themselves. (See: all the mages' collective quests - essentially, you policing blood mages before the templars have to get called in, and keeping templars from going too far, and so on.) DA2 also adds to this in Legacy, and Bethany's story - basically if your freedom meant THAT much to you (which to some people it does, much more than not being hungry or having safety) then all you needed was to keep yer d@mnfool head down and you were fine.
I'm just going to note here that Anders was definitely NOT a mage I'd have considered safe to leave wandering around. He wasn't the threat the templar hunting him claimed, at least not back then, but he totally failed at 'low key' and a lot of his commentary suggests he felt, even then, that mages were naturally superior to everybody else by dint of having magic. ("I'll show you why mages are feared!")
The templars in Kirkwall are no more generally representative than the mages in Kirkwall of how the Circles usually work - the mages are being affected by Kirkwall itself, the templars are being affected both by the mages' uncharacteristic behavior and Meredith going wonkers from the lyrium idol; the war begins there because everything that CAN go wrong with the Circle system, DOES go wrong - the templars fear the mages and so more or less imprison them. The mages, hated and feared by the templars, start turning darkside just to survive or find a way out, and the mages in turning darkside justify and enhance the templars' fears, thus hello spiral that ends in massive boom.
The circle system could only exist as long as the mages were willing to accept its existence. They're not rabbits. They have genuine power. They refrained - in most cases - from using that power for the same reason the circles exist at all; mages in most cases don't want to BE abominations.
But neither can 'mages' be categorized in a single way. The system worked best when it took that into account - that some mages are fine if left to their own devices, some are best if kept away from worldly issues, some can't have power without wanting to use it to rule, and so on. Mages are people; they're no more and no less corruptible than the average human being. We've had ethical rulers and leaders, and we've had corrupt tyrants. Once the system started trying to force All Mages into a single position it was *bound* to fail.
And - again at the human level - some people being born with power and some not has a tendency to lead to a fear reaction. That templars who had faced blood magic would fear all mages is absolutely understandable. That they were kept on duty to police mages who had - up to that point - shown no signs of ever wanting to use blood magic, is not. It's just...an inevitable spiral, which I think has kinda been the point of the games thus far. Seeing the dark side of magic leads to an understandable fear of the potential of any mage to go there. Acting on that fear makes mages more likely to lash out than they otherwise would have been; lashing out justifies the fear even more and leads to greater repression, which in turn leads to more lashing out, until boom.
I don't think DA3 will force a pro-templar response. At least I hope it won't. What I really hope for is that there is a reasonable alternative; some way to let those mages that can and want to either retreat from society a la the old Circles, or live in the world as battlemages or healers or whatever, without necessarily ruling it a la the Imperium. Any blanket solution is going to result in mages for whom the solution is a poor fit, which while typical of the games thus far, would just mean revisiting this conflict in a later game. And frankly, while I do think this conflict merits a few games - so do several other conflicts we've seen outlined in Thedas thus far.