I don't get too attached to any one side. Some PT's I'm pro-mage. Some I'm pro-Templar--at least in sentiment. And truth be told, the whole mage/templar thing is going to be a small part of DAI. And it will be resolved rather early in the game.
I tend to veer towards whatever sentiment is most in line with my character's personality, rather.
My Warden was horrified by what she found when she saved Redcliffe and the Circle from demon-possessed mages. But her sense of fairness demanded that those mages who were still fighting Uldred should be saved, rather than destroyed on some off-chance they'd been compromised themselves. She had a vivid notion of diplomacy, justice, and tact, being the daughter of a Teryn.
My Hawke, on the other hand, was far more aggressive, to the point at times of being caustic and brunt. He fought alongside mercenaries, even. His earliest life was marked by his father's admonishments that magic was dangerous and needed controls, he accepted his brother and then his friends to keep an eye on his own self in the event he failed to control his own magic, and he generally wished more often than not he could just lose himself to the Circle rather than constantly watch over everyone. He sided with the Templars in the end, if only to avoid fighting against his brother.
Me personally? I'm not neccessarily opposed to either the mages or the Templars. But I tend to think the world of Thedas as it's been described is one where (a) magic is dangerous and requires control and (2) the Templars as they're supposed to be are the best agents in place for the safety and security of everyone, including the mages. I'm waiting to see the story continue to unfold before deciding how my Inquisitor is going to act, is all.