I kind of took for granted that he'd figured it out at some point. After Ben died, Kaine went after the Scriers and them.
My problem with this issue here is that Kaine decided to make his peace with Ben and atone for his past a long time ago. And back when he thought Peter was a clone (which I guess is still the case), he was very protective of him, thinking of him as kind of a little brother who'd made good. He seems unaccountably hostile here.