My PoV is thus: When choosing the lesser of two evils, you're still choosing evil. Both sides are complete drama queens. I have played through twice (first siding with mages, second templars) just like the OP.
I would be more on the mages side were it not for the fact that Orsino supplied Quentin with the books and knowledge necessary to perform the f***ed up necromancy. Since that plot line is solid and unchanging, it's okay to have a rooted, stubborn opinion.
It would be easier to say for sure one side is right and one is wrong were it not for the complete extremist that Meredith is and the ambiguous extremism that Orsino shows. A sadistic part of me kinda wishes there was a "Kill 'em all" choice when and if a gamer chose templars once and mages once, but that's quite a stretch.
As someone previously stated, the Templars, seemingly, have an "AHHH! It's a mage! Kill it kill it!" approach and the mages act the totally innocent role. Yet, in the scenes that show mages turning to blood magic, there's no showing of the mages using magic prior to being backed into a corner. One would believe that if there's, say, 5 Templars, attempting to kill and/or corner a mage, that mage would be able to take out AT LEAST one of those Templars. Alas, it only shows the mage defending his or herself with blood magic.
Unfortunately, all the Templars like Cullen are overshadowed, and outranked, by the likes of Meredith. And Anders' decision is on par with, if not worse than, any action Meredith had taken previously. As bad as Meredith is, I've decided to take the Templars side from here on out.