I can sypathise strongly with the OP and some of the responses here.
I began my playthrough as a mage-Hawke basing his attitude to mages mostly on what we were told about his father - ie an apostate but one determined not to bring attention to themselves or cause collateral harm. As such I went around trying to be supportive of mages where possible especially when you get told how terrible the Kirkwall circle is for mages and how Meredith is ridiculously draconian soon after you arrive. But my Hawke didn't approve of blood magic (which is something of a hypocrisy as he ended up in a relationship with Merril but unfortunately the game didn't give you any option to talk her out of blood magic at this stage.)
But by the time of the final confontation I was on the brink of siding with the templars anyway. The sheer amount of insane blood mages you encounter really makes you wonder if they are all beyond saving, and that you are the only who isn't turning to blood magic and demons (and no I didn't have blood magic specialisation

).
Then your mother is killed by an insane blood mage.
Then Merril ends up killing Marethari and her whole clan - some keeper she turned out to be. And this is one of your companions.
Then Anders blows up the chantry, murdering Elthina who had been nothing but kind and reasonable throughout the game. At this point I felt the argument "not every mage is bad" had been used a few too many times to remain entirely credible. But I still sided with the mages because Orsino was just as vocal in condemning Anders as everyone else and was a good mage and a voice of reason, making Meredith's rite of annulment insane. I killed Anders, despite supporting him throughout the game in his views. Some things theres just no excusing.
What really pissed me off is when defending the mages from the Templar assault is Orsino suddenly becoming another insane blood mage and turning himself into waaagh-blob-monster-from-hell. There wasn't even a proper reason for doing it; the champion was with him and the waves of templars were getting repulsed. When does "I'll turn myself into a mindless blob-monster incapable of distinguishing friend from foe" become a viable option in this situation? While fighting my way out (through more insane blood mages and abominations mainly) I was half hoping for an option to just tell Meredith she was damn well right all along, but then she turned out to be bat**** insane as well.
I think the overall moral of this story is - sometimes the only options you have are bad ones. And that the Arishok was right the whole time.