The only way I could justify siding with Meredith at the end is if you're playing a non-mage-Hawke and Bethany died in the Deep Roads. Even then, you still have the issue that even Sebastian sees: how is annulling the Circle justified when the person who just blew up the Chantry wasn't in the Circle in the first place?

Not turning Merrill in could be rationalized by hoping you can convince her she's wrong. Anders is a bit trickier, although you could argue that locking him up means that a lot of people in Darktown would end up dying without his services. If you keep him from killing Ella, then on balance, he's helped more people than he's hurt, at least, up until the endgame.

(Ella is one of the big reasons I can't side with the templars, because I just can't send her back to the Circle. Her story indicates that either Meredith is letting her templars do whatever they want, or she's not paying enough attention.)