I really don't get this, you are mad at Bioware because some idiots decided to behaves like jerks ?
The flashpoint you ran 15 minutes before arriving to that convo is centered around you "killing" (not hitting or mistreating, but killing!) hoards of men and women, but head butting the captain with a rifle is the only thing you find questionable and misogynistic ? Just because of some idiot sitting behind his PC ?
If so then you are employing double standards and you should complain about every dark side choice that leads to an NPC being mistreated.
In fact, I find portrayal of women in this game to be fair. They are portrayed as senators, leaders, generals, military personnel, thieves, spies, murderers, heroes, there is no discrimination between how men and women are portrayed. The misogyny is only within you and not on the screen!
I think it's more of the context at which they do the action.
Like they probably laugh and say crap like "Wish I could do that in real life LOLZ" or something stupid like that.
I've seen it happen so many times.
It might be a bit double standardish, but it's extremely annoying to see it. Usually when I see it happen, my troll mode activates, and it all goes downhill from there.