While Star Trek TOS showed a very progressive society for its time, a few major exceptions stand out. Specifically the series finale "Turnabout Intruder", where Star Fleet was shown to be prejudiced against females in command positions. Was this ever retconned or addressed later on in the series? Was it just Star Fleet or the Federation as a whole that had those prejudices?
Generally speaking Women in TOS were supposed to be treated the same as men in-universe.
In fact, according to Teh Internets, T'Pau (a female Vulcan) was apparently offered a position on the Federation Council (she turned it down).
The show was written in the 60s, however, and some sexist perceptions of the time very well might have been written into the script.
TOS never really was that big on plot continuity anyways.