In the case of my canon Hawke, I think there's an important distinction to make between "taking Meredith's side" and "agreeing with Meredith". For one thing, it's possible to spare quite a few of the Mages if you take her side (including Bethany, and several others who explicitly surrender, plus, presumably, any survivors from after Orsino went down). For another, and related the passage quoted above, it's very possible to believe the Meredith is part of the problem, but also decide that Mages have gone "too far", and you can only handle one issue at a time.I'm replaying through the game at the moment, so someone correct me if I'm wrong, but does Hawke encounter any non-party Apostate mages that aren't evil? It's possible to know Orsino was supporting Quentin back in Act II (although, as noted, the exact extent of which is not clear, but at best, it's implied Orsino didn't care anyway), and the only "good" Mages I can recall offhand are Grace's group, who turn out to be lying anyway. And in the party we have Bethany (okay, yeah, she's pretty innocent), Merill (who's not deliberately evil, but is dangerously foolish), and Anders (who just got finished blowing a sizeable chunk of Kirkwall the **** up). And that's not even getting into Leliana and her Tevinter conspiracy. I feel like Hawke has a lot of justification for assuming the Circle as a whole is not salvageable by the time the end of the game rolls around. And while s/he might feel that the Templars are similarly problematic, just nuking both sides at once isn't an option.
I definitely see what you mean, and I can understand a player (and their Hawke, by extension), deciding that they had just enough of Kirkwall mages and them constantly holding the idiot ball. Even Hawke himself declares that with the right dialogue. And there's also the (very logical) counter-argument that, even if Orsino isn't as responsible for Quentin as he's made out to be, he was certainly responsible for the mages that were in his Circle, And he failed in his duties just as badly.
I guess, one other thing that rather tips the scale just a bit more against Meredith for me was comparing her with Gregoir in the first game. Gregoir, at the sight of the first abominations, sealed the door and awaited for instructions. It's true that he wasn't that hesitant to agree with a warden to clean up the tower when the chance was offered, but he probably figured that he didn't really have any authority over them. And yet, he's shown as reasonable about it, and if you help the mages, he doesn't give a What the Hell speech nor does he try to kill you over it. Unlike Meredith.
But as I said, I can see why people side with her, and I don't consider the option 'evil'. I just can't choose that option for myself and my Hawke.
(ETA: A rather logical, albeit flimsy, reason that we don't get the chance to see a 'good guy' mage, for lack of a better way of putting it, is that Varric probably didn't consider those kind of encounters relevant to the story he's telling Cassandra. He's trying to explain how Kirkwall reached its breaking point along with Hawke's involvement, thus he keeps the things that he believes are crucial. Except that well, a narrator isn't necessarily reliable, not out of malintention, but because that's how he interpreted the situation.)