We've got that covered - you must have missed the "1993" origin.
Well, that was from the Comic based on the cartoon which was the old origin dressed up to look like redbeard's version to please DC
Not quite - this origin is from 1993 - the animated series didn't start until 1996, and the spin-off comic book,
Superman Adventures, didn't start until 1997. In that Universe, the origin had been told in the pilot episode, and it looked nothing like this story.
At the time, the most controversial elements here were that Jor-El and Lara liked each other and had good physiques; Superman had powers as a tot; and that he had short hair (instead of a mullet) as an adult!
"Superboy’s Darkest Secret!", from Superboy No. 158 (July 1969), by the team of Frank Robbins, Bob Brown and Wally Wood, would probably have to be the most controversial retelling of Superboy/man's origin of all, and is probably regarded by most learned fans as non-canonical.
With a statement like that, you've got me curious what happened in it that's so controversial!