On the other hand, mages have been abused by authority most of their lives. Do you really think they're suddenly going to allow some relatively unkown faction that appears to be on the chantry/templar's side in the mediate their problems? And even if the mages somehow get a favorable outcome, what guarantees they keep it that way?
Keep in mind that mages were ruled over primarily by the Templars, not the Chantry. Given the attitude of their leader, and that an apparently large faction of them looked at Meredith's incident with red lyrium and thought "Wow, a magical substance that drives you homicidally insane? Yep, time to start using that and turning into our own variant on abominations," is it any wonder they saw open rebellion as a better choice then any diplomatic option? It really doesn't help that Templars are apparently fully within their rights to murder every mage in the Circle if they feel like it, given they've tried it in both DA:O and DA2, whereas mages have no such protection against radical Templars.
Edit: I'm sure not all Templars are overzealous and morally reprehnsible, just like all mages aren't bargaining with demons and cackling evilly at every opportunity. And even though we don't actually see it in any of the games, presumably not every Circle is a horrible place to live. Most likely there are instigators on both sides who would like to see an open conflict, and arrange events so that the mages have no choice to rebel. It's not really the fault of any one group, but really just a questionable at best system being abused, with a lack of oversight exacerbating the problem.