This is such an interesting topic for me, when I first played DA2 I was pretty young and naively thought "OMG Poor mages are being treated unfairly! Not all are bad!" and Harry Potter was really big then so you can't blame me lol
Then I came back to DA2 2 years later, and realized... whoa... I'm making so many pro-Templar decisions.
The threat of any mage becoming an abomination means their MUST be someone able to control and watch the mages. Templars. Mages themselves cannot be trusted to do this, since they obviously failed to do so in the Ferelden circle. Not to mention, Templars are invisible to fade spirits unlike Mages, who apparently shine like a beacon.
I guess you could call me Aequetarian; I want the mages in a circle, I want them to be brought there to study and learn. But I don't want it to be a prison; I want it to be their home. When they prove they are wise and trustworthy, they'll be allowed to freely roam whatever city the tower is in, if there is one. Eventually, they'll be able to have complete freedom, so long as they report back to their tower regularly and the Templars always know their destination.
The whole problem with mages is that cruelty and lack of freedom drives them to want more, and they use their powers to get what they want. Which causes more hatred and suspicions from the Templars, which makes them stricter; vicious cycle. If Templars could be seen as guardians rather than jailors then the mages wouldn't feel the need to rebel so much.
In short, given the chance I will likely side with sane Templars rather than sane mages.
When it comes to Red Lyrium Templars; that's no excuse not to side with the order. Red Lyrium drives anyone, even dwarves insane. Imagine what it could do to a powerful mage. BTW, I'm not siding with Red Templars; they're insane and need to die. I'm siding with what the order stood for.