Then disregard that point and consider that, despite some opposition to posters here, she is still the leader of the Mages and is managing them like Cullen and Leliana. Do you notice that Ser Barris doesn't get any War Table missions after he's promoted?
Barris' whole point of War Table missions is to restore Templars' good name, to earn back trust of the people and to show he is capable of leading Templars, he does not really need missions to prove anything after he gets promoted, he has already proven that he deserves the title by doing a lot of good. Fiona is already a leader and a crappy one at that, her previous mistakes also dont show her in a very good light.
While I do agree with you that situations for Mages and Templars are similar and both have the Inquisitor to the rescue, its the details that got me on Templars side.
The Mages that went before "rrrawwrr, freedom!" are now covering in Redcliff and hiding behind their incompetent leader. They do not object. They whine, while Templars fight the corruption. They submit consciously to slavery while Templars die rather then become monsters. There is a reason we do not see Barris when Haven gets attacked but we see Fiona. Because Barris died fighting and Fiona just submitted. And then after the quests finish from mages we hear "but its time magic, we were forced!" and from templars we hear "yeah, it was our fault, we screwed up, but we are willing to make it better".
This isn't very eloquent reasoning but in a nutshell its pretty much what I thought.
Edit: Personally, (as much as I dislike Fiona) I thought it was a horrible way to kill her off as a mini-boss in the first part of the game, I actually felt sorry for her character. I thought she was built for something grander. Even Samson got more screen-time than her, and he was a hopeless lyrium addict.