As long as I can remember I didn't interpret it that way. We had seen positive examples within the series that suggested women could rise higher in rank and unless it's actually spelled out otherwise I took it to mean they could achieve command rank.
But not all TOS episodes were written by the same people with the same sensibilities. Shows weren't staff-driven back then so they could represent a multiplicity of voices and attitudes, even with a producer like Roddenberry rewriting most of the scripts himself. For instance, Kirk was often less successful in his seductions in episodes written by women -- e.g. "By Any Other Name" (co-scripted by Fontana), wherein Kelinda is more amused by his seduction than overcome by it and ends up becoming the aggressor with her own preferred boy-toy Rojan, or "Is There in Truth No Beauty?" (by Jean Lisette Aroeste), where his attempt to seduce/distract Miranda bombed completely.
But Roddenberry was responsible for not only "Turnabout Intruder," but the story behind "Mudd's Women," an episode which implies that women have no prospects in life at all beyond being wives or sex objects (despite Uhura's token presence, the male crewmembers act as if they rarely see women on the ship, in keeping with decades of military and space-show cliches). And he co-wrote "Bread and Circuses," in which Kirk raises only a token objection to spending the night with a sex slave. Some TOS episodes are more sexist than others, but the very worst examples all seem to be in episodes with Roddenberry's name on them.
Which, really, is strange, considering how willing Roddenberry was to give Dorothy Fontana a prominent role in the show, a role that's no doubt largely responsible for the more positive portrayals of women we got. He also cowrote his Planet Earth pilot with Juanita Bartlett, which is a good thing, since I think her perspective helped the story dodge a lot of sexist pitfalls. I don't think Roddenberry was consciously sexist; I think he really believed he held a progressive view toward women and their equality. But he had a lot of strongly gendered attitudes and assumptions that I don't think he could entirely see past. Which isn't surprising for a man of his generation, living in that decade, so he can't really be blamed for it. He tried to be progressive, but he wasn't nearly as progressive as he probably believed he was.