Siding with either the mages or the templars doesn't mean you are endorsing that side. It just means you've enlisted their aid against the breach.
Really? It doesn't feel like the line is clear here compared to Origins. After Dragon Age 2 it feels like you're damned if you do and damned later if you don't. I resolved the Dalish/Werewolf conflict by not conspiring with either side and ended the curse. That could be resolved again peacefully in DA:2. I chose Harrowmont for dwarven king and I didn't have to deal with it later. Killing Avernus and the possessed body of Sophia Dryden didn't haunt me either.
But in Dragon Age 2 it's like you can't get a break.
I spare Dupuis and Ser Emeric dies later. I don't spare him and Sir Emeric still dies. I spare Dupuis and Leandra still can't be saved. I spare him again and all I get is an apology and a small item.
I help the refugees of the Starkhaven Circle get away, and they kidnap one of my companions years later and try to kill me. A good templar dies either way. I don't help them and I'm an oppressive jerk.
I help the workers of the Bone Pit and it still gets razed by a high dragon. What the heck?
The good thing about a Blight is how it brings people together.