I think you're wrong to interpret the essay as a joke. It's a logical extrapolation from the Silver/Bronze Age assumptions about Kryptonian powers. At the time, the premise in the comics was that Kryptonians were just like humans, except that when anything Kryptonian was exposed to yellow sunlight, it became superpowered. And I mean anything -- people, animals, metals, fabrics, minerals, you name it. That was the rule in the comics at the time the essay was written. Niven did what any science fiction writer would do: he started with that speculative premise and deduced its logical consequences. If what the comics said about Kryptonian powers were true, then this would logically be what would happen if Superman had sex with a human woman. It was no more a joke than the comics themselves were a joke -- which means that the underlying premise was fanciful and played for fun, but the intent was still to tell a coherent narrative based on the established rules of the setting. The comics themselves did a lot of the same kind of extrapolation about the consequences of Kryptonian powers and the superstrength of Kryptonian materials; Niven was doing the same thing, but with a subject matter the comics weren't able to go anywhere near. Its humor lay in the juxtaposition of such adult and explicit subject matter with a wholesome comic-book character written (at the time) for children. It doesn't mean the logic of the essay was intentionally invalid. It was an entirely valid extrapolation from what the comics of the day had spent decades driving home about how Superman's powers worked.
True, later interpretations of Superman haven't used the same explanation for his powers; the "everything Kryptonian becomes super under a yellow sun" principle vanished after Crisis on Infinite Earths. But that means that different portrayers of Superman are able to interpret the nature of his powers in many different ways. And if they choose to follow the logic of Niven's essay, then they're perfectly within their rights to do so. It's not "wrong," it's just one possible interpretation.
And it's a logical one. Even if we ignore the stuff about super-strong sperm and whatnot, there's still Niven's point about how orgasm involves involuntary muscle contractions. A being with superstrong muscles might be able to control those muscles carefully enough to keep from hurting people under normal circumstances, but when it comes to involuntary muscle spasms, all bets are off.