Course the fact that Lois could even have Superman's kid blows... literally... Niven's "Man of Steel, Women of Kleenex" theory.
Only half of it, that she would be unable to carry a superfetus to term. Apparently, the lack of yellow sunlight in the womb helps in that regard, as does the fact that the baby is half human.
But, it does nothing to dissuade us from the belief that Superman's shotgun-like ejaculation would completely annihilate Lois if they had sex. The only reason they were able to make love in Superman 2 is that Clark gave up his powers and was no stronger than a mortal human at the time.
And that's as good an explanation as any for why Superman left her after getting his powers back.