The whole thing is messy. On the one hand it could, like Rucka is doing now, be used as meta commentary on issues in the real world and fandom's view of Superman/Clark/Lois. It lets Lois in on the joke so to speak subverting some of the silver age tropes that a lot of people like to pretend she never moved past as a character. We'd know the people ragging on Clark and Lois aren't right, and they'd be likely be portrayed as in the wrong.
But on the other hand, in universe, if you're not in on the joke it looks and will be acknowledged as it should be. Lois will have conned Clark into marrying her and raising Superman's kid. All while she's sleeping with another man. Superman himself will actually look pretty terrible as well And rightly so. He'd be lying to a supposed friend in Clark and taking advantage of him. It's not Superman behavior at all. It just doesn't leave any of them looking good.
I think that is why Clark will have to be shown to have been in on it publicly and they go the step parent route. It still allows for some.people to wrongly criticize him and Lois. It adds a wrinkle to Jon's life and Superman's but it doesn't quite literally tarnish all the characters in the public of the DCU.