I really think the game was written to make you sympathetic to Templars. You either get betrayed or see firsthand how unreasonable or sick the average Kirkwall mage is. Meridith plays up this angle too with your mother to get you on her side. And if that isn't enough, you find out that the First Enchanter was behind your mother's death all along.. that his whole "innocent mage" act was a lie. He's a blood mage way before the final battle (Hope you don't mind these spoilers.. I'm assuming you've moved on from playing the game again).
The only good reason (imo) to side with the Circle is if you were a warrior or rogue and Bethany is locked up there.