I sided with the Templars.
On my third playthrough.
With great, great wincing pain and a touch of personal shame. I had great trouble sticking to the character I was playing (someone deeply scared of abominations, enraged about Quentin and Anders and Grace, and thinking it was better to put the mages out of their misery.)
While I like Cullen and Thrask and quite a few templars, I can't condone what Meredith wants them to do. Genocide--the murder of human beings whose only crime is to be born as they are--is horribly, horribly wrong no matter what. Even after what Anders--one individual possessed mage--does, even after what Quentin the blood mage did, even after that stupid bastard Orsino who let Quentin do his thing lost his damned mind, even after that stupid evil spoiled brat Grace, the bulk of mages are still frightened innocents constantly threatened with death and several fates worse than death (possession, tranquility, being some templar's sex slave in order to avoid him abusing his power to get them made tranquil). Even the bulk of blood mages and abominations are composed of scared fools who felt their only other options were worse than turning to horrors. It's hard not to sympathize.
The one thing that mages who DON'T succumb to the dark side of magic have in common? Emotional stability. Wynne, Irving, presumably the Amell or Surana who saves the world, Hawke and Hawke's ancestors, Bethany... hell, even Emile de Launcet. He was silly and foolish, but he had a loving mother and father who accepted him as he was.
Mages who aren't condemned for being what they are; mages who aren't treated like monsters, who weren't raped or tortured and aren't monsters innately incapable of understanding morality, like Quentin--they don't turn to the uglier side of magic. And that, in and of itself, is pretty clear proof that the templar system does as much harm as good.
There must always be templars, but not fanatical zealots. Templars like Cullen was, and is at the end of DA2. Not foolish enough to trust the wrong people, like Thrask, but certainly not anything like Meredith either. Templars who respect life and understand balance, who don't assume that magic is a stamp of evil on a human soul; a sign of the Maker's disapproval. Templars whose aim is to protect not only normal people from mages, but mages from each other and themselves. Friends to mages and to humanity in general, not enemies.
I think DG is right; that the vast majority of people see siding with the Templars as they are in DA2 to be a form of genocide. Equivalent to joining the KKK or snuggling up to Hitler. I could hardly stomach doing it at all, and even then I felt sick for doing so.