I would find it interesting to see how Saeko being willing to bow down to a man could be considered a flaw by anyone other than a female supremacist. My take is that she just doesn't see herself as 'leader' material for some reason. I do think she has an idea of what a 'leader' ought to be though and she sees some of that in Kuromo and tends to encourage him to embrace it in her own way. Whatever it is that Saeko is reacting to I certainly don't think it's as simple as him having a penis.

She makes me think of a soldier looking for a worthy commander to follow. She has her own head and her own ideas but lacks (or suppresses) the internal spark needed to take the reins and blaze her own trail pulling everyone along with her. Instead she defers to Kuromo and only offers council and analysis, leaving the final decisions up to him. Considering she could kick his ass or browbeat him into obedience with her seniority and maturity I think it takes a lot of self-discipline for her to behave the way she does towards him.