Even if such an unlikely event happened (I don't believe women couldn't competently Captain a starship and I'm not even a lib, we have chicks commanding stuff nowadays, are they all failing miserably?) the PC LIB Federation would never draw that conclusion and make the decision to outright ban vaginas from the Captain's chair, even a more common sense orientated government would be unlikely to do that.
And as you say any woman who's an officer is in the chain of command and could end up in charge of the ship. It just doesn't make any sense.
Do we really want that to be canon because of one line from one silly (but enjoyable) episode? All of the things that might be wrong with this show I don't know why that would bother anyone.
There are 2 choices, take Janice Lester's statement at face value and try to make a ban on female Captains fit into the narrative (I can't make it fit for me) or do a very soft retcon chalking it up to Janice being nutso, and she WAS seriously nutso, so that's an easy choice for me.
It’s possible the ban was made with respect to top-of-the-line starships (Heavy Cruisers and Dreadnoughts) and that it was a ban “reviewed” every so often (or perhaps even a “glass ceiling” thing where women COULD conceivably serve, but never qualified).
It would be curious to see where Commander Chapel (Number One’s) went from the Enterprise. She might’ve been promoted to serve as a captain of a lesser ship (Scout, Destroyer, Light Cruiser, Frigate). One could even envision that she made the breakthrough and was the cause for officially removing Dr. Lester’s cited “ban.”