Really? How interesting. I've always tried to make peace with them. Elder Pavus (good term, easier than continually saying Dorian's father) seemed to realise that he'd gone too far and both he and Dorian were hurting. It just seemed that trying to reconcile them would put Dorian's mind more at ease than just leaving without even talking about the problem.
I always have them make up too.
Maybe it's my own experience coloring my perceptions, but Halward Pavus reads as someone who genuinely does love his son. He got caught up in a society where "doing a blood magic ritual to change my son's sexuality" seemed like something that might make his son happier in the long run. The last resort of good men. That was wrong, of course, but I think he had good intentions behind his bad actions.
Once he realized he'd screwed up, he tried to seek forgiveness. He fumbled a little on how to ask forgiveness, fell into the old pattern of arguing at first. He argues because he's scared that the magisterium will tear his son apart (in Trespasser, he arranges for Dorian to be out of Tevinter when things get hot), the way my Evangelical parents argued because they were scared I'd go to Hell. But goddamn it, Halward is trying to understand, and that's something.
Making up with parents isn't for everyone, and people should do what's best for them, in these kinds of situations. I have Dorian talk to Halward for my own sake.