It wasn't justified; it was wholly unnecessary. Only demons had to be killed. As is the case for all Annulments; that's why it's never justified, because the right wouldn't be necessary if demons were the only beings you were killing.
It turned out not to be necessary, but it was justified. The Rite of Annullment is invoked when a Circle is found to be beyond saving: the last line of defense for the Templars. It it is very, very rarely invoked (what a dozen times in a thousand years?)
In the case of Ferelden, the Templars were barely holding back the demons, who were rampaging through the tower and possessing mages left and right. It's only because of the aid of the Warden and the personal assurances of Irving that the Annullment was made unnecessary.
And even then, the Warden can point out that demons may still be lying dormant in some of the mages. Irving will agree to that and have the mages put into voluntary seclusion until they can be examined by outside sources (it's the only way to get Templar support without anulling the Circle) CUllen, especially given his firsthand experiences, had every right to be concerned.
And many things more. How many does he realize? Like his apologetics for Tranquility, even the Tranquil Solution.
You realize that the Rite of Tranquility is meant to be an alternative to killing mages, right? It's supposed to be a way to spare a mage who can't handle their power without putting them to the sword. And there appear to be very clear rules on who is to be made Tranquil. It's still obviously a highly flawed answer, but that's why Divine Justina was looking for another alternative.
As for the Tranquil Solution, I don't think Cullen was for it, or even took it seriously. All he says is "some have made an argument for it" And mentions it was shot down by both the Grand Cleric and Meredith (before she became the mayor of Crazytown) Cullen seems to be for Tranquility (again, as a means of sparing a mage's life who cannot handle their powers or demonic temptation) but not as a "Solution"