I think that is so there is something for Hawke to hate the mages at the end. Because the First Enchanter is behind the murderer.
I know. But if you sided with the templars and fought the first enchanter, it revealed that the first enchanter actually knew the killer and helped him from being discovered. That's also the reason for Bethany to rejoin the Hawke's side in the fight against the enchanter and the knight-commander.
I think that the mages are actually more devious. Take Anders for example, he used Hawke to assassinate the Grand Cleric. The First Enchanter supported Hawke's mother's killer. Most of them dwelt in blood magic, even Merill whom I loved.
The templars were only controlled by the crazed knight-commander. Not that they actually wanted to suppress the mages so much.
[Edited by owlet, 3/14/2011 8:28:19 PM]
[Edited by owlet, 3/14/2011 8:34:45 PM]