I don't think it is screwed up at all.
The punchline should come at the end of the sentence. And "helium" is funnier than "hydrogen".
The important part of this sentence is not the example, but the claim:
"Humor is a universal element."
That is the point to get across, so it comes first. The example is a humorous element, it wasn't necessary at all. And choosing a universal element to compare to, hydrogen and helium were the first to spontaneously form from the energy in the Big Bang, and between them, helium is funnier than hydrogen.
Helium makes people talk funny. There is very little humor centered on hydrogen.
You were right to begin with, Harlon Ellison (or was it J. Michael Straczynski? He wrote 92 of the 110 episodes himself) is a great writer.
Perhaps the name for messing up sentences like that is "burying the lede." It doesn't make sense to bring up the analogy before making the claim.
It wasn't supposed to be a real example, clearly the way it was written, Captain Sheridan was adding an afterthought, and a humorous one. As if he said "universal element" in the sense of a universal trait, and realized element had a literal meaning as well, and compared it to the literally elemental helium for emphasis.
That was funny, IMHO, and the punchline is at the end.