Eh, Meredith could have called an Annulment much earlier if that was always her intention. After all, Meredith still considers Mages to be children to watch over hence why, even in her insanity, she didn't try and annul them until after Anders destroyed the Chantry. She was also right that the people WOULD demand blood and that's exactly what happened. The only way to curb the chaos was to step up and Mages were the easy scapegoat as Anders was a Mage and Blood Mages have been terrorizing the City for years. Not to mention that much evidence pointed, rightly, that a lot of Blood Mages came from the Circle itself.
Actually, Meredith was seeking authorization to call for the Right of Annulment much sooner than Anders' little endgame, as indicated by Ser Kerras if he survives the encounter with Hawke at the coastal approach. It was only until The Last Straw that she decided to take it upon herself to invoke the Right without it.
As for the idea that the people would demand blood, this is something I deny entirely as proper justification for anything. The people can demand blood for just about any silly thing imaginable; that doesn't necessarily mean that it's something that should be respected and followed through by the authorities. It could be something like wanting to kill all mages in the city for the crime of one, or something a bit more down to earth like wanting to wipe out or subjugate a certain race or religious order for the simple fact that they disapprove of their existence. Either way, I won't honor it, regardless of the risks. If that means casualties, then so be it.
You can spare surrendering Mages if you side with the Templars as the Templars deeply respect Hawke thus they differ to Hawke over Meredith. It's why Meredith doesn't push the issue if you try and spare Bethany as well because Meredith knows that Hawke is very popular and that not all the Templars under her want to kill all the Circle Mages even when that is their orders/duty. They simply wanted to restore Order to the city and were grieving over the loss of the Grand Cleric.
The fact that certain mages can be spared never factors into my decision, because it requires metagaming for it to do so. The option doesn't exist until after the fact, so the option simply does not exist at all. When the execution of every mage is called for, I must assume that there are no exceptions, regardless of any objection on Hawke's part. With that and the fact that I believe that the Circle was not complicit in Anders' crime, I have no choice but to oppose the order. Aside from their grief over the loss of the Grand Cleric and any Templars in the Chantry, restoring order to the city is not my primary concern, especially if that means leaving the city under the rule of the Templars, regardless of the chances of success.
It's a reality of the situation that Hawke siding with the Templars ends up with a better Kirkwall as Hawke, due to their popularity/influence, is able to calm the populace, be put in a position of real power to enact changes, and can convince the people and the Templars that not all Mages are evil by sparing Mages/Bethany or being a Mage them-self as the people want Hawke to lead, if Hawke sides with the Templars, even if Hawke is a Mage.
I don't really know what a "better" Kirkwall looks like, because I don't really get a good look at the city in the aftermath, and it kind of doesn't matter anyway, because the Circle system is already collapsed and the two factions are already going at it. That one filthy little city with a rotten power structure might make it out with a bit more polish is not terribly meaningful to me, but just the same, it's still a matter of what I can reasonably expect when making that first decision, and when choosing between Templars and mages in The Last Straw, whether or not order is restored to Kirkwall more quickly or a new leader is firmly established in a shorter amount of time are not my priorities.