Is there any substantial contemporary evidence at all that Roddenberry made choices on the original series as if it were a dramatization of real events? Because that would be a truly deluded creative process, pretty much doomed to failure. Not only was he writing and producing fiction, he was doing it in a very specific production environment with regard to studio and audience expectations. The Making of Star Trek documents him as making clear-headed and practical choices with budget, resources and the rules of drama and of the television format foremost in his mind.
Insisting upon plausibility - i.e., "Would a real naval officer do this?" - is quite a thing apart from pretending that anything in the stories really happened or might ever happen. In fact, the answer to that question as posed had to be "No, but it's the way storytelling works" whenever a choice had to be made.
It's been said that "But this really happened" is the worst reason for putting something in a story, but the obverse is just as true: people seek out fiction, particularly fantasy like Trek, in pursuit of that which can't be experienced in reality.
