Perhaps this is a touch too sentimental and romantic but I can't help but see it as the only valid solution.
For each Mage, a Templar. The Circle should exist for the purpose of education, yes. Without the Circle, Mages would be completely wild, unpredictable and uncontrollable. At the same time, you're completely right about Mages being vilified and hated, and being reduced to animals by the more cruel Templars out there. They need to be able to leave thier cage, to wander the world and learn so that they can gather more knowledge for the benefit of the Circle and society as a whole. Of course it isn't wise for them to do this alone so... why not have a Templar bound to them, in a way? Someone to accompany them and aid them in everything that they do and to chastise and restrain them if they ever threaten to endanger society with their maigc. Equal yet not; with the Templar subservient to the Mage until the Mage is a threat to those around them, and that is when their Templar is in a position of authority and the Mage is the one that has to obey.
Of course there are obvious issues with this. A Templar could become emotionally attached to a Mage so perhaps they'd need to be rotated? A new pairing with every year or something along those lines. I know that there's literally no chance of this compromise being seen in DA:I but I can't think of any better solution, while keeping the Circles as they are. The Templars would have their place as guardians and enforcers while the Mages would have unprecedented liberty in Andrastian Thedas.
Mage poisons the Templar's beer while he is in the bathroom. Problem solved.
Mages have the freedom to "wander" Thedas once they have proven they are trustworthy. Think Wynne, Irving, Ines, Finn, Rhys, Adrian, Bethany, Mharen, Orsino, etc.
Finn is the best example, I believe. He just walked up to the Templar in charge, asked for permission to acompany the Warden and it was granted to him? Why? Because the Templars know he not dangerous, he is not entertaining thoughts of escaping or controlling people's mind and he is very young so it's not like it took him his whole life to earn that trust.
People like Anders, on the other hand, are placed in solitary for a year because they don't even try to earn the Templar's trust. They just assume that because normal people are free to come and go from their homes when they please, that mages should too despite the fact mages are dangerous.
In resume, mages have a very good home that they can only leave if they can prove there is little chance of them harming someone. Given they are extremely dangerous, this doesn't seem like such an unresonable system, at least as far as freedom of movement is concerned.