I think the idea is that Isaac actually loves his son, but is really awful at showing it because he’s bought into all this nonsense about how a noble should behave. Plus, he has a temper. He flew off the handle and disowned Elymas because he was disappointed and felt his hand was being forced because the head of his house “had” to be a swordsman or related class, and he probably went off to cry in private afterwards—or so the writer(s) would like us to believe.

Anyway, he wasn’t the one who wanted that confrontation—he originally asked the butler to take care of it, remember? Malice was the one who pushed for him to come down hard on Elymas. It isn’t clear whether he went along with that to please her because she’s now his heir and they have to work together, or for some more emotional reason that he would never admit.