I do disagree. This doesn't surprise me, they like to throw around the accusation like candy, but its not misogyny. It just means the guy did his historical homework. Bendis is playing off the very, very common past historically narrative that a Kryptonian and a human can't procreate. It seems to be being drawn attention to now as a plot point regarding Jon's existence. People have wondered if it might be brought up since he was created, and now it seems to be. It has nothing to do with misogyny and everything to do with tackling questions of genetics between two differing species.
As far as Jor-El himself, despite his crimes as Mr Oz., the last Superman had saw of him, he had just broken his staff and realized there was something messing with his mind. They were even in the process of a "moment" before Oz was teleported away again. So I don't see anything odd about their interaction here. Clark is still obviously wary and untrusting, but he at least knows he's not insane anymore. That fits with where we left off. The only thing not being acknowledged is the supposed mystery of what made Jor-El disappear at the end of the Oz Effect in the first place.