I guess the difficulty, as usual, is in the fact that there are no whites and blacks here, just shades of grey (*cough*). And even that simile is problematic because it suggests a stable state, whereas the real world is dynamic. What may begin as 'mostly good with bad bits' (Justice untempered by mercy) may quite easily end up as 'mostly bad with good bits' (mass murder sparking a catastrophe which may ultimately lead to a better world state).
I personally detest the self-righteousness and moral absolutism that Anders/Vengeance fall into by the end of DA2, coupled with an equally absolute 'whatever it takes'. While I have utmost sympathy for the mages in 90% of my playthroughs (freeing Jowan, letting him redeem himself, saving apostates from templars in DA2 etc.), I fail to ever feel anything but hatred for Anders at the end of DA2. I suspect that even his displays of guilt are nothing but an act that serves to stylise himself into a martyr of a cause nobody but a few, equally despicable, mages share (e.g., Uldred). And that is even worse for me because I absolutely adore Anders in DA:A (and share his cause, most of the time).
P.S./Edit: To elaborate: Kirkwall is clearly an outlier in how mages are treated in Thedas. The situation is not good, but still quite tolerable when Hawke arrives in KW. It deteriorates at a slow pace until the red lyrium warps Meredith's perception of reality. Other numerous circles show that templars and mages can find a workable, if uneasy, balance somewhere between mage predominance and templar predominance. In fact, we are shown quite clearly in DA:O that putting mages on one side and templars on the other is not the right way to look at it; ultimately both parties share the same goals, like the two hands and two eyes a body uses to interact with an object
Yet this one act of "freedom fighting" (blurgh!) destroys freedom not only for most mages, but most templars and most innocent bystanders as well. It's not freedom fighting at all. It's a rash and brutal act of impulsiveness, free of any moral/ethical considerations. Like all demons, Vengeance acts on emotions alone, not on a well-thought-out analysis and consideration of alternatives. And everybody but him pays the price.