As I said, you have to consider the context of the times. Having women on the ship at all
was a major step forward. But there were limits that '60s writers and audiences weren't ready to cross yet, for the most part. Progress comes one step at a time, not all at once.
It reflects what was going on in society at large around those times. The idea of women in the workforce was becoming more acceptable, but it was still assumed that it was the purview of single women, and that they'd give up their careers when they got married (an unquestioned assumption we see reflected in McCoy's lines about Carolyn Palamas). In The Avengers
, Mrs. Peel was an accomplished secret agent as a presumed widower, an icon of female empowerment for her time, but in her final episode, her husband turned up alive and she gave up the spy game to go back to being a housewife, just like that, no questions asked. It was just a given that that was what a married woman did.
And by the same token, TOS could be progressive enough to include women on the ship, but not enough to put them in command positions. They could be portrayed as partners or subordinates of male officers but not superiors -- not unless they were exotic Others like Romulan commanders. Not because there was some formal policy statement against it, but just because it didn't occur to them
. There were assumptions they made that we question when we look back on them, but that doesn't mean they questioned them. Maybe they didn't consciously object to the idea of women in command, but it didn't really occur to them to try it either.
It's a lot like the non-portrayal of gays in TNG and after. Roddenberry made noises about how it was "time" to acknowledge that gay people existed in the Federation, and there was never any formal policy against it, but the producers were just never strongly enough motivated to depict it, and made excuses for avoiding it.
So no, there's not going to be some smoking-gun memo formalizing the glass ceiling. That's not the sort of thing it was. It was more a sin of omission, a failure to look beyond certain preconceptions.