Write Away

Ahhh, I can understand where you're coming from. Most of my stories feature women in "nontraditional" roles, but when I start thinking about it that way, I start worrying if I seem like I'm trying to make a statement, and "women are so badass and cool" is just as bad as "women are conniving and evil" because these traits should be completely separate from the actual gender of the character.

I don't think you should worry about making the villain a woman. Try not to even consider it mattering, focus on the character beyond the gender. But a good general rule is that if you're worried about making a social statement with a character that's going to be reduced to his or her group, then have another character from that same group that's not in the "controversial" position. If your villain is gay, that's fine, but if you don't want an audience to suspect you might be homophobic, have at least one other gay character who is a hero, or at least as more admirable traits. Same with a female villain - are you able to make another female character on Joshua's side, who also perhaps has those traits of being clever and charismatic, but isn't a villain?

I think equal representation definitely applies to villains, too. Or rather, I don't like to think of it in those terms. More just writing about real people who happen to be fictional. But it is important not to reduce the character to that particular trait or group status, and better to have other members of that group present in the story who are not antagonists. Especially if you, the author, are not in that particular minority group yourself.