This particular foxhole had kept out Ogres and Emissaries, and while it comes uncomfortably close to failing as the Warden arrives it's not like it's facing anything like the same threat this time. I'm surprised they thought they needed more security than that.
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.
But I'll agree that it's surprising that the Templars are still trusted. If Leiliana was right and not just biased in favor of anything Chantry.
I always thought that very strange considering how Leliana was pushing for the mages.
And your last point? The problem is that human rights are a concept that are suspended if the need arises. People who are sufficiently insane (and insane in the right way; ie dangerous) can be forcibly put in a hospital. People who are sick with something contagious are put in quarantines, and not all of them like it. I'm pretty sure that potential abominations are about as dangerous, at least until they've earned some trust. Maybe you'll come up with an argument that changes my mind on this, but it's not going to be anything like this simplistic because this issue is by design not a simple one.
Now, I do agree with you that the Circles should allow some freedom. Mages who have earned some trust should be allowed outside to work and maybe work off some degree of the distrust that common, ignorant people have of them. We've seen that people can get over their justified distrust of magic, or at least make an exception to it, if they owe a mage their lives. Why not let mages try to earn some of it, while spreading the word that they owe it to the proper training given by the Circle? This system might very well help keep mages from going untrained their entire lives or being lynched before they can arrive for training.
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.