In defense of the blood mages it was out of self-defense and fighting for their freedom. I don't know how becoming an abomination helps matters but the games wants us to believe they do to fight their oppressors.
Everyone has a choice including the templars who help Meredith. They could refuse the order since she wrongfully invoked the rite of annulment. In the end Cullen does finally stand up to her although he should have done it sooner.
I didn't understand for example why he supports her but hesitates killing those 3 mages. Yes, they surrendered. So did all the mages under Orsino. Meredith refused and wanted the whole Circle annulled. The only difference is these 3 are willfully putting their heads on the chopping block. Why spare them? Why spare Bethany? Yes, Hawke wouldn't want their sister to die but it's very hypocritical to help murder all the other mages but not her because you care about her. You think those other mages Hawke strikes down aren't someone's sister or brother? If you're going to be an evil bastard by helping the templars why do players think letting Meredith kill Bethany then is going too far?
I also wonder how much better Kirkwall is for aiding in the unjust slaughter of the mages. Think about Emile DeLauncet's family for example. How will the nobility feel that their children were killed ironically to appease them? Many would be outraged. And how will this influence people sending their children to the Circle in the future; knowing they might be sending them to a slaughterhouse?
I'm sick of people calling this evil. How can so many people be ignorant to the concept of self-defense? On my first playthrough I did this completely unintentionally because they attack you if you say the wrong thing. On later playthroughs I did it by role-playing what I would say in that situation, which was to point out that Marethari was possessed; still earning the Dalish' wrath.
The templars have no grounds to go against Meredith, even Cullen who suspects her madness all the way at the start of Act 2 which is after she got the idol, because there are Blood Mages and Demons all over the streets. Furthermore, a Mage literally blew up the Chantry in front of their eyes mere moments ago. Whether they felt all Mages are bad or not doesn't change that the Chantry was gone and there are Blood Mages and Demons all over the place. The Templars did their duty to try and restore order against the Mages since whether Meredith is at fault or not for pushing them they were still Abominations everywhere.
None of them has more authority in the order in Kirkwall over Meredith. Cullen couldn't act until it was proven beyond any reasonable doubt that Meredith had lost it. He couldn't challenge her when she evoked the RoA as the Templars, rightfully angry over the death of the Grand Cleric, would side with Meredith. Despite that the Templars will spare Mages, who surrender, if Hawke is with them which says a lot about how they started to feel about to RoA after Orsino tried to surrender and Meredith wouldn't have it.
Because the Templars didn't have the stomach for killing those weren't resisting. Orsino is a different story, they know he hide Blood Mages within the Order and the Blood Mages running all over the place are Orsino's responsibility. It's hard to forgive the figurehead, who knew about the Blood Magic abuse for years, while it's far easier to forgive and not want to kill those who are literally innocent and begging you not to kill them.
The point is this, while the Templars are a lot of things it was the Abominations that tore apart the city and whether they did it in self-defense or not doesn't change that the people know this - A Mage killed the Grand Cleric in cold blood, a Mage destroyed the Chantry and everyone inside, and Mages are summoning Demons and using Blood Magic in the streets while the Templars are protecting them from said Mages.
So it's as I say, it's morally right to defend the Mages but it's in Kirkwall's best interest to aid the Templars.