So far, in both Origins and DA2, whenever forced to make a choice between mages and templars, my three Wardens and two Hawkes have ultimately supported the mages: both in the Circle Tower and in Kirkwall. I've mostly played characters who were either mages themselves or otherwise sympathetic to mages, and/or were opposed to what they saw as unnecessary killing. In general, the portrayal of the mages as an oppressed minority resonates with me more than the idea that they are dangerous and need to be contained, so that's the way my characters tend to lean as well.
My first Hawke, rogue Marian, was a little more moderate in her opinions than the others -- she believed in working with the templars she saw as reasonable, and wasn't always gung-ho about freedom for all mages. If I'd been given a little more player freedom, Marian would have tried to use her influence to get Meredith ousted years before endgame and installed Thrask in her place. In her canon, Bethany went to the Gallows and was at the very least content there; Marian was in a relationship with Anders and loved him dearly, but she wasn't completely convinced that the future he envisioned was the best one for everyone. She didn't pick a side until the very last moment. In contrast, my mage, Marissa Hawke, started out without a strong opinions on the subject -- no one was going to lock her up in any Circle, but she wasn't particularly interested in fighting for anyone else's freedom. But as she gained influence, and began to see the unfairness of her ability to walk free while others did not, she grew more supportive of Anders and his cause, (though they were never anything other than friends), to the point that she was openly speaking against Meredith and the Chantry by halfway through Act Two.
I do want to play a templar-supporting Hawke at some point, because I'm curious to see the story play out through that lens. But having successfully saved Ferelden's Circle three times, and knowing how simple it is to do so, it would be hard to bring myself to justify annulling it just for the sake of one quest outcome. Maybe someday, if I roll up a hell-on-wheels Warden, a character whose entire plan is to bulldoze their way through Ferelden, not much caring whom she or he hurts along the way. Part of me thinks that would be fun -- I had a blast playing an aggressive Hawke -- but given some of the choices an anti-hero Warden would have to make, I don't know that I could follow through.
Complete list of questions
This entry is also posted at http://owlmoose.dreamwidth.org/572840.html. There are currently comments on DW.