lol...I want to quote Carver... "Great.. another precious mage flower." 
The measures people will take to protect mages. Creating some global military organization to control even religion itself.
I think you misinterpreted what i said.
Its not to protect mages, its that they are a great asset for combat and authority. If the authority figure handles magic with responsability, he is more powerful, not someone who is a afraid of the unknown like the templars.
I would gladly and openly Recruit Darkspawn or Demons if they were reliable, but sadly i have to settle with the Mages, since they are the more reliable of the bunch (and the only option present in the game).
I recruited the Mages under the Inquisition's thumb, they are not free 
The problem that i see with the Chantry is that its just this political body that does not help the Inquisition to achieve domination, i see the Chantry as much as a enemy to the Inquisition than Corypherous.
Thus, i support the mages because magic opens up new possibilities and a more offensive capabilities, instead of defensive ones like the Templars. Along with the fact that i openly challange the Chantry's authority with that decision.
We probably play diferently, but in DA:I i felt like i was conquering southern Thedas through influence and military power, not just to to end Cory/The Breath but to impose a new Order in it.
Oh, and just so you know, i dont even play as a Mage 
But yeah, i want a global military organization, i aint doing it in name of mage freedom (although mages may get freedom as a side effect) but more in the name of order and justice (and tottaly not because my Inquisitor has megalomaniacal tendencies).
So yeah... Order & Justice looks much more noble than "I WANNA RULE THE WORLD!" 