Saying that she deserves it means nothing when she can't get it. Its empty sentiment when it amounts to "you deserve freedom but there's no way you can actually ever get it within this system that I endorse so too bad I guess."
I'd say it's more due to the nature of the people doing the supporting that they support it.
Who said I endorse/support this system? There's lots of middle ground between the status-quo and libertarianism. Bethany is what pushes me away from status-quo. Merrill and Anders, OTOH, are what chuck me away from the libertarian persuasion like a hot potato.
And consider exactly why Anders bombed the Chantry - to expose the inherent injustice of the circle of magi, to fight for magi liberation. He is not waiting for anyone to give mages freedoms - that is a fundamental problem in this and it will never happen anyway.
What Anders thinks or wants does not matter. After he got "Justice"-nonsense in his head he stopped having any good ideas and the Templars should have executed him before he (predictably) killed lots of people in a fit of angsty pique.
Freedom is a right all mages have as men and women and there should not be exceptions for those deemed worthy by society that hates them collectively. Its a repulsive approach
And yet, not as repulsive as the Tevinter Scumperium, where all mages are free on principle as you advocate.