I've played entire playthroughs of DA2 with the idea of siding with the Templars at the end, but when Meredith decides to annihilate all the mages just because the one who blew up the Chantry is standing right in front of her and she somehow decides to ignore that in favor of destroying what she has always hated ... I just can't do it. It makes her just as much a monster as Anders. Both characters are basically acting out their hatreds. They're basically using one thing as an excuse to do what they've always wanted to do.
For Anders, he's striking out at the innocents in the Chantry instead of Meredith and Templars who are truly at fault. He justifies it by saying that Chantry refused to take a side, but in reality, I don't think he wanted them to. If they had, he would have to take a risk that they would have actually sided with the Circle against Meredith ... after all, the Circle's complaints were actually just. By removing the Chantry, Anders removed any hope of resolving the situation by removing the third party that could have laid the whole thing to rest.
Meredith in turn used the Chantry explosion to justify her removal of the Circle once and for all. Who cares that the Circle hadn't actually done it? All that matters to her is that she can justify the leap in her own mind.
So the dominoes fall, but I don't see how you can fall out on the side of Meredith. There are children in the Circle Tower, even if your sister isn't in there, the children are. Do they deserve to die because of Anders?
Well, let me take that back. I did manage to side with her once. In one playthrough because I wanted to see how that road ended, but it made me feel dirty.