I'd be on the men's side. Preferably in the background in a more tactical or technical role (or alternatively, and what would be more likely, some form of driver or pilot), but on the men's side none the less.
I'm pretty damn sure I'd be accepted. I seem to be accepted in "real life" without any issues (I've been on T a while, I live day to day without revealing my background). I see no reason why it'd change for a hypothetical situation.
I sure wouldn't be accepted into the women's team, anyway!
I would feel no obligation to even consider joining the women's side. I don't consider myself female. I can't feel any sense of betrayal towards a group I've never really been a part of.
I suppose my response would be more interesting if I wasn't all uncool and binary fitting, but ah well... I am what I am!
Besides, there's always a chance an all man army might start "going greek" - especially after all the women have been wiped out. How could I not fight with that side?