Ha, ha, ha... it's funny when an episode's original meaning is twisted around to fit what a person wants to see rather than what it really is.
I know. I did it with Star Trek: Enterprise because it is a horrid show that doesn't make any sense in the context of the Core Trek Time Line.
However, there is no good reason to take an Original Series episode out of context. Kirk doesn't disagree with her or look at her funny when she says what she says. In fact, he agrees with her that it isn't fair.
Kirk isn't treating her like an insane person. He is treating her with openness, honesty, and genuine care.
I mean, honestly. Show your parents and friends this episode and have them pay close attention to this scene. Replay it for them again at the end if necessary and ask them what they think this scene means before sharing your hypothesis with them.
Also, the show was made when women were not accepted in certain leadership type positions in the work force yet.
Clearly the series is a reflection or product of the times. That is one of the reasons why the pilot episode "The Cage" was not aired in the first place. The network didn't believe a woman should have had a leadership role on board a starship. And no. It wasn't because she was Gene's girl friend either. Here is a quote taken from Making of Star Trek Pilots.
Adding to the scenario, Nimoy explained, "The network eliminated one character entirely, the role of Number One...They told Gene to also get rid of the guy with the ears, insisting that the audience couldn't identify with an extra-terrestrial character. Gene battled this but was finally forced into a compromise. He felt the format badly needed the alien Spock, even if the price was the acceptance of 1960s style sexual inequality. A new pilot was written and Mr. Spock was in Number One's place as second-in-command as well as having some of the woman's computer mind qualities. Vulcan unemotionalism and logic came into being."
"The reasons were these: too cerebral, not enough action and adventure," he said. "'The Cage' didn't end with a chase and a right cross to the jaw, the way all manly films were supposed to end. There were no female leads then--women in those days were just set dressing. So, another thing they felt was wrong with our film was that we had Majel as a female second-in-command of the vessel. It's nice now, I'm sure, for the ladies to say, 'Well, the men did it,' but in the test reports, the women in the audience were saying, 'Who does she think she is?' They hated her. It is hard to believe that in 20 years, we have gone from a totally sexist society to where we are today--where all intelligent people certainly accept sexual equality. We've made progress.
Oh, and also, Assistant Managers can carry out General Manager duties. Doesn't make em General Managers, though.
Quoted Source:
http://www.earthsmightiest.com/fansites/startrek/news/?a=6323