Go for it. Anything can be done so long as it's done well.
The key, like with race and sexuality, is to ensure that characters are well-rounded, but also so that there are more than one examples of them. For instance, if you just had one woman in your comic and she was weaker than everyone else, all the time, then that would be bad.
But if you give her strengths in other areas and ensure you have other empowered women in your story, you are giving multiple shades of representation.
In comics like this, women will fight men. Sometimes they will lose and sometimes they will win. Don't make it gratuitous and just ensure she will get the upper hand at least half of the time (although, really, with a hero, you want this to be most of the time).