You're talking about a group of people with no military training against one of the best armed forces in Thedas, one they have a good reason to fear, considering they'd been (in their minds) imprisoned by the Templars. I'd be terrified too. Add to that the fact they believe that everyone in Thedas thinks they killed the Divine. This was their last stand.
You don't imprison a person based on what they might do, and the truth is that the slippery slope can go the other way. We've seen it before.
St. Augustine of Hippo called for the Jews to be an eternal "witness people" to be allowed to survive but not thrive. What came after was well... we all know the stories.
Yes, I realize that it's not a one to one, but the basic idea is the same. How long does it take before someone starts asking "why are we bothering to keep them alive?"
I'm not arguing that mages need training. I'd think a more "guild" style Circle would work, but the idea that they have to be completely isolated without lives... It just exacerbates the problem the Chantry is trying to prevent. Mages have no stake in the world, and have no real idea what it's like to live IN the world. So they're willing to commit to insane and stupid risks because they have nothing to lose and think everything will be rosy on the outside.
If they weren't capable of rebelling intelligently, they should not have rebelled. And if they had no acceptable option but rebellion, Fiona was not an acceptable leader.
And the comparison you're drawing with Jewish people isn't merely "not one to one." Mages are capable of throwing fireballs and lightning, and my Jewish friends assure me only trained Mossad agents can do that. If mages are feared, they're also necessary, unless you think Thedas cares to handle the qunari, the darkspawn, and the Tevinter without them. If Jewish people had any purpose in the Middle Ages and Renaissance, it was because they were forced into money-lending, and they occasionally had that (and the money) taken from them. The mages cannot be discarded, because if you take the magic from a mage you don't have magic that can be put into someone else. You have a Tranquil.
The Circle I have in mind would be like the ones that allowed Vivienne to do what she did, unless you care to argue she had no stake in the world. Of course, I'd hope the Templars would have more brains than to allow someone with no willpower, and who they're pretty sure literally couldn't pass the Harrowing to save his life, into Val Royeaux's court. Since, you know, my main argument for the Circles isn't purposeful abuse of magic.
Mages need education, need training in their powers, but they DON'T need to be locked up in a prison.
How about a quarantine?