Carriers of an incurable contagion of unknown vector. What choices did they make that would meet your criteria?
People who are mentally incapable of caring for themselves, and as such are confined to strictly controlled facilities. Where is their choice?
In both cases, freedom is the worse choice.
There are plenty of other examples. Freedom is not a universal good, nor is it even universally desirable.
To your first, that is not a permanent solution, meant only to last until the contagion has run its course.
To your second, that only applies to people who have shown signs of mental incapability, been tested and found clinically unable to take care of themselves AND a danger to their families, and are locked away because it's been proven. And even then, we are making advances that are decreasing the frequency this happens.
I happen to have pretty strong feelings on your second example, because if I had been born 20 years earlier, I would've been one of those people locked away.
The point is, freedom is good except in exceptional cases, like in the contagion where thousands, maybe even millions will be harmed as a result of the disease, or in the case where individuals have been proven dangerous to themselves and others.
You may say this is why the Circle's exist, and I agree to an extent as young and untrained mages really are a danger to themselves and to others, but after they're trained and can control their powers, all the Circle's ultimately do is take away their rights and freedoms based on what might happen because of what they are and not based on who they are or what they've done.