When she called for the annulment, the reasons were there for her call to be valid. Yes, she used Anders as an excuse, but that only speaks to the fact that official channels failed.
That Annulment was not justified in that it punished the collective whole for the crime of someone outside of that group.
Meredith's argument for the Annulment at the time she asks Hawke to help her, is not blood mages. It's not magical corruption. It's not even the mages role in Thrask's rebellion to oust Meredith.
Her one and only reason to appeal to the Champion for aid with the Annulment is "magic has destroyed the Chantry. The people will demand blood." That is her entire argument for Annulment at the time she calls for it.
As such, being right about Orsino being a blood mage or hiding blood mages, and there being blood mages hidden in the Circle is irrelevant. When she says "the people will demand blood because magic killed the Grand Cleric," and Orsino says "The Circle didn't even DO this!" I'm more inclined to side with the mages in this conflict because they are not being punished for something they did or even for corruption in the Circle. The stated reason at the time Annulment is called is because the Grand Cleric was killed by magic and Meredith was going to give the people blood.
So her reasons for calling Annulment are irrelevant because she gave none of those reasons at the time she called it.
I'll ask you a question I find startlingly relevant here.
Does it honestly matter? These mages became what people fear from mages, demon summoning, mind controlling, walking abominations. If the answer to that question to you is yes, then I'll ask another. Does what they endure justify that? If not, then what is was the purpose of it? How does using blood magic, summoning demons and alike actually gain them freedom?
How does vengeance become justice? If you will forgive that horrible pun.
If your answer to the first question is no then I'll simply conclude with this.
Kirkwall dug its own grave, regardless of what drove them to it, what justification they had.
By reacting as they did, they condemned themselves in the eyes of their own institution.
Oh you mean the ones who weren't murdered in cold blood by a mage?
It matters in that they are people who, ought to be treated with a certain level of caution simply because of the nature of magic itself, but they are people nonetheless, and most of them are not guilty of any crimes.
Vengeance isn't justice, as Anders clearly shows, but desperate acts aren't vengeance either. There are quite a few court cases in real life where desperation or acting under duress got them off the charge. It's circumstantial and changes from person to person, but in many cases in Kirkwall I feel Templars, or the corrupt ones, were the driving force behind most of the mages acts. There are a few cases where you have a genuinely bad mage, but the vast majority of mages I saw in DA2 were desperate because of how heavy-handed the templars were, and how the punishment pretty much always went far beyond the crime.
And let me ask you a question.
Where is the justice for every mage who suffered at the hands of a templar who abused their authority over mages?
Justice, as a concept and not the spirit, punishes only the guilty in accordance to the severity of the crime. If a mage is living in the Circle and isn't breaking any Chantry rules or laws, and gets raped or illegally made tranquil by the templars, then justice dictates that the templar in question punished.
Justice is not one-sided. It punishes the guilty regardless of status. It doesn't deal in grey. Only black and white, absolutes. It cares nothing for if the guilty party or the victims is a mage, templar or a farmer.
So yes, I say it very much matters, at least in regards to Kirkwall I'll always support the mages there, not because I support blood mages or abusing magical power, but because they suffered unjustly at the hands of a corrupt system that will not punish its own.
The templars have shown, through their abuse of authority, that they are not fit to be the caretakers of mages in the Circles. They have become too corrupt and biased due to centuries of religious fervor and practices.
And no, I meant the Chantry leadership in Val Royeaux, the ones who oversee ALL templars and Chantry practices, and supposed to oversee the Seekers. The Divine, and her aids felt that Meredith's call for Annulment was unjustified.