SGB I think you take this kind of thing far too seriously. Do you have a lot of overbearing male influence in your life? I have never experienced inferiority due to being female. I've always been equal to guys - but in fact I haven't seen them as anything superior that I have to be equal to.
We are all just people, fair enough there are societies and historical periods where men have dominated (and indeed some still do), but there is no reason for this. It's just a way of living that has become ingrained in those particular societies. I think feminism can go too far the other way though, and try to make women superior, rather than recognising everyone as equal.
Also, men and women can and should be equal in many ways, but nothing will ever change the fact that they have basic differences, mainly located around childbirth. I think it's a shame when being "traditionally feminine" is belittled, and women who don't do "manly" things are somehow making themselves inferior.
But I digress...
OP - I think there's nothing wrong with tomboy, it's just a word that people use to describe someone subverting gender stereotypes. You don't need to believe in those stereotypes though, in which case tomboy is utterly meaningless and shouldn't annoy you at all. I have no issue with ds painting his nails with felt-tips and walking round in my high heels, even though MIL says it will turn him gay . I also have no issue with him playing football and being loud and boisterous. Kids will do what they feel happy doing, and won't consider it wrong unless you tell them so.
I was a "tomboy" and still am - dh is more "feminine" at times.