Nope, it makes sense - when you remember that, at the point of Act 3, Anders is The Cause™. He is in full “if you are not with me, then you are against me” mode. Witness how he responds if Hawke refuses to distract Elthina - he says outright “I have always been alone. I just forgot it for a time.” He asks for Hawke’s unquestioning loyalty, and then gets pissy when Hawke expresses concern for him.
DA2 is, for Anders, the story of a downward spiral. Act 3 is when he is jumping all the way off the slippery slope. So to him, the injustice of slavery pales in the face of the mages’ rights, and Fenris is an obstacle to that. So if he’s out of the picture, all the better for The Cause™. Mages need to be free MORE.
Likewise, and on the more individual level, Fenris has, in Anders’s mind, always been the greatest rival for Hawke’s affections. Anders has a narrative in his mind - he is The Hero, fighting the Great Injustice, in the name of the Greater Good. And in that narrative, The Hero is supposed to get their Great Love. Anders puts Hawke in that role early on - whether or not Hawke returns his feelings.
And of the other romances, Anders views Isabela as impermanent (since she’ll exit the game entirely in Act 2 if you don’t get her approval high enough) and Merrill as doomed to death by way of her blood magic (never mind the irony). Sebastian is in the grey area, given his status as DLC, but he’s also the DA2 party member most at a distance of the group anyway.
But Fenris? Fenris is loyal. This is the man who will wear Hawke’s favor regardless of if Hawke continues their romance or moves on to someone else after what happened. Fenris is committed. Fenris will stay.
Fenris is his rival. Fenris is the obstacle to Anders having his “Great Love” in the form of Hawke.
Anders is a selfish person, a selfish character. He always was. Hedonism was a major character trait of his in Awakening. But, when Justice joined with him, he couldn’t think only of himself as an escaped mage. He picked up The Cause. But that selfishness is still there - he’ll say that Hawke is what he wants, regardless of Justice. And he wants to get the obstacles out of the way of him getting Hawke.
Fenris is one of those obstacles. So he’ll gladly take the opportunity to get rid of him.