Roddenbury apparently admitted that the story was sexist at some point
and taken at face value the comment about Starship command is certainly so,
That said, as someone has pointed out Lester is crazy for coco puffs so its not hard to retcon the statements.
In fairness I get the idea that Kirk and Lester were in a relationship that was quite toxic, with Lester, though being brilliant and intellegent making a lot of demands on Kirk ( notice that Kirk invariably seems to have a history with highly intellegent women, most Scientists) and he just got sick of it and dumped her. Its actually a kind of counter balance to his relationship with Carol Marcus, who he would have stayed with but her love for her own career ( as opposed to jealousy fo his ) got in the way.
Would have been great to see her play against number 1 from The Cage though.