No, she was not.
She wanted more restrictions towards mages - yes. She suspected Orsino of hiding Blood Mages and possibly being corrupted himself and rightly so. But she didn't want to kill them all - provoking her is on Anders' hands. Starting this war is on Anders' hands. Hundreds killed - Mages, Templars and civilians alike - that too is on Anders' hands.
He was so blinded by the ideas of "freedom" that he didn't realize that freedom isn't the same thing for everyone - and that some may value peace higher than freedom. But in his arrogance, he felt that HE of all people was qualified to make this decision for all mages in Kirkwall Circle.
That's very ironic - he spoke of freedom, yet he forced the fate he chose on everyone.
Yes, she actually was. Karras' dialogue in Act 3 confirms it. I don't remember the exact wording, but it's something along the lines of "Knight-Commander has sent for Val Royeaux for the Rite of Annulment. The robes are going to get what's coming for them. Soon." [the last two sentences I remember really well, because they were rather chilling in their enthusiasm]. This is also evident in the way she acts after the Chantry explosion: she says the Grand Cleric has been "slain by magic" (not: an apostate with no ties to the Circle who just admitted doing it), and calls for the Rite. On the Circle that had nothing to do with the explosion. Which is trying - desperatedly - to work with her after Anders' little bonfire (Orsino says: "Search the Tower, I'll even help you. But don't judge us all for an act we did not commit." Meredith is like "... Nah. I'd rather just kill you all.")
She has the culprit right there. And she decides to do nothing about it because she'd rather get rid of the Circle (plural) than Anders.
It's quite clear she has lost her head ages ago. The only person who could've done something about Meredith was Elthina, and she chose not to. She not doing her job and governing the Templars is what led to mages being terrorized in the Gallows. Anders couldn't get to Meredith or the Templars in general because their headquarters are in the Gallows along with the mages, but he could do something about Elthina. And that's why he blew up the Chantry and not the Templar barracks, for example.
Also I kinda wonder how Anders chose anyone's fate for them: he just gave them a new option. Every mage in the Gallows was going to die either way (Meredith was pretty insistent on that Annulment): Anders just gave them the option to fight and liberate themselves. He proved them one crucial fact: that in the large scheme of things, their innocense of guilt is irrelevent, that their lives are in the hands of the Templars, and if the "situation" demands it their heads will roll, no matter what they have or haven't done ("The people will demand blood" is Meredith's justification). Again, if the situation hadn't been that bad in the other Circles, the mages there wouldn't have had any reason whatsoever to join this rebellion or associate with it in any way, shape or form. If Anders hadn't had any cause and there'd been no need for his actions, there wouldn't have been a reaction at all. All the other circles who rose up either
- because the mages there were attacked first by the Templars after the Kirkwall Rebellion because the Templars thought offence was the best defence, or
- because the life in the other Circles is not all fun and games and the mages (or majority of them) chose freedom over the Chantry. (Actually they even voted to leave the Chantry in Asunder, and although that vote didn't go down in the best of circumstances [understatement].)
And: if the Templars and the Chantry had taken his and the other mages' complaints seriously (as in, look into how the Circle operates when they found out that one of the Templars had been abusing the Rite of Tranquility to build his own private harem!) and had dealed with them, Anders wouldn't have had a leg to stand on.
Bolded part: yes, that's exactly the point. DA2 is a story which ask which you value higher: authority (and safety/order) or freedom (chaos). It's about the balance between individual rights and the common good, and what freedoms (and, what people) are we willing to sacrifice to archieve what we deem the perfect balance. "Is submission not preferable to extinction?" Agree, disagree? To what degree? Who is allowd freedom, who's not? Under which conditions and rules? Who makes those rules and gets to decide how free you are, or aren't? Should we be able to punish pre-emptively to protect the possible victims? We see both what the mages are capable of and the measures Templars take to "keep the mages and the general population safe", and we're asked: is this too much? Not enough? Who's in the right? There's a lot going on under DA2's hood.
EDIT: Woah, this was not supposed to be this long! Sorry about the massive TL;DR Wall of Text.