I can just see it. "Guys, here's a story about one of Kirk's former lovers really out to get revenge on him. And while we're at it we'll contradict three years of positive role models for everyone and concretely establish that women don't have what it takes to be starship Captains and can never hope to be. Oh, we'll also be ignoring what we established way back when the series was being developed as well as that little episode earlier this season that showed a woman commanding a squadron of starships. But of course she was alien and obviously superior to human women."
But that's the thing -- prejudice isn't a conscious decision. What's insidious about it is that it's unthinking, so even people who imagine themselves to be progressive can still have a lot of prejudices they haven't realized they have. By the standards of the 1960s, including women on a starship crew at all
was progressive, but that didn't overcome the unexamined assumption that women would naturally fill the traditional roles of secretary, nurse, and the occasional scientist or lawyer, while men would fill the traditional roles of command and security and hold almost all the senior positions. They challenged one
of the preconceptions of their era -- that women couldn't be allowed to serve on military vessels -- but they unthinkingly embraced another set of preconceptions -- that there was a natural difference between the roles that men were suited for and the roles that women were suited for.
So you're right that it wasn't the conscious
intent of the episode to assert that women should be excluded from command -- because that was something the writers didn't think they needed to assert. It was the default position that they accepted without thinking -- that men and women naturally have different specializations. The point that Roddenberry was hamfistedly trying to make was that, even though women's roles are different from men's, that doesn't mean they aren't valuable in their own way. He was going for a sort of misguided variant on ST's "It's okay to be different" message, saying that women didn't have to adopt male roles in order to have self-worth. We can recognize today how many unexamined preconceptions were blinding him, but it was too close to the everyday standards of the time for the episode's makers to realize how condescending they were being.
It's important to have a historical perspective about these things, to recognize that prejudices are overcome incrementally and that attitudes that were progressive in their own day can be extremely backward by today's standards. So we have to take care to evaluate a creator's intentions in the context of their own era's attitudes rather than our own.