I'm pro-Mage always. Mike Laidlaw (Lead Designer on the Dragon Age Series) says it boils down to: Liberty vs. Safety.
*Spoiler alert obviously*
Normally I'd say "liberty", but "liberty" in this case is for the freedom of mages. Aside from Merril, nearly every encounter you have with a mage in Dragon Age 2 ends with them becoming a blood mage, consorting with blood mages, and so on. Even if you go full kindness and side with mages at every opportunity, doing everything in your power to protect them and be nice to them, even the
first enchanter becomes a horrible abomination that takes your entire well trained and armed squad to take out. The Templar were right: The Circle of Magi had to be purged in this instance. They
were corrupt to the core.
That being said, you were confronted with the same option in Dragon Age: Origins, and after choosing to save the Circle of Magi, they turn out to not only
not be a bunch of malificarum blood mages, but help you save the noble son in Redcliffe via magic. Yet, still, the Circle of Magi in Ferelden wasn't controlled in a tyrannical fashion: The First Enchanter and head of the Templar were close friends, with the Templar being sympathetic and the Mages being understanding. This is especially clear in the character of Wynne: Who is a wise, understanding old woman that tries to help guide you without forcible controlling you.
In Dragon Age 2, it's far more black and white and extreme. The Templar were right: The Mages
are a bunch of malificarum far more often than not. (Even Merril consorts to using blood magic and doesn't appear to learn anything after it pretty much spells the end for her entire clan due to
her actions.) On the other hand, the Templar are paranoid and operating in a tyrannical fashion, and there are instances where you can see mages turning to blood magic because they feel they have no other choice to survive under their rule.
To summarize: Liberty is a meaningful quality among men, but when certain men are born with superhuman powers that give them a far greater chance to go insane, certain liberties must be curtailed. That being said, a healthy, mutual respect with sympathy from the caretakers and understanding from the mages is necessary to sustain such a relationship. Fear and paranoia only causes terror, which leads to stupid people doing stupid things, like turning to blood magic. For those that scream out "liberty for mages!" I ask you, if every psychotic on Earth suddenly gained the capacity to manifest their darkest desires upon the world, and the only thing keeping them from total madness is willpower, and demons turned out to be
real and
constantly testing that willpower to possess these people, would you sincerely be comfortable with letting thousands of biological superweapons held together by piano strings to walk the Earth as freely as everyone else? Or would you try to gather them together to keep not only the public safe from them, but them safe from the public?
"Equality" is only meaningful when all parties are truly equal. Mages are not.