That doesn't prevent them from leaving, they are quite more then capable of leaving either the Chantry or Templar Order.
Seriously, i find it highly inaccurate to label it in anyway shape form of the Chantry "owning" those Children, when once they have come to adulthood they can remain or make their own way.
It isn't denied to them, and in the mean time they have a place to stay, education and food.
Sounds better then what a lot of Thedas endures daily.
And have their choices made for them, the very thing Alistair talks about during his time in the Chantry. And that made it the thing he resented most about the templars and the Chantry.
And when it comes to mages, having material goods, shelter and food does nothing to prevent abominations, blood mages, or any of the dangers that magic poses if the mages does not have emotional stability. The mage origin shows this clearly at the beginning, with that mage practicing with fire and setting himself alight because he panicked at hearing of injuries, or that apprentice who is told straight out by his mentor that fear is the enemy when it comes to the strength of his fade shield. Wynne also talks of losing her temper and setting a childhood bully's hair on fire.
Giving mages material goods ultimately does nothing to help them control their powers and resist the dangers that come with being a mage if they are kept in conditions that prohibit emotional growth, and often times inflict emotional suffering, like a mother mourning over a child taken from her at birth, to orphans wondering what their parents were like, or even the children who were abandoned by their parents simply for having magic, like Jowan, and then watched constantly in a system that does not really hold templars accountable for abuses of said mages.
Yes, they have better living conditions than most, but if they lack self-esteem, a strong emotional foundation and stability, the Circle will ultimately fail at their intended purpose.
It's not right to create crappy emotional conditions and treat them as monsters, and when they lash out in either desperation or self-defense, to use that reaction as justification for treating them so badly to begin with.
I'm all for reforming the Circle system, and reforming the templars, but I will never condone punishing mages for something they haven't done, nor breaking up families if it can be avoided.