I think it's a question of if you are making her intentionally unappealing or actually trying to highlight the appealing side of her that is not the looks. It will be clear you made the character so the people will need you to show them something spectacular about her other than the appearance. As long as you'll be able to do that you won't disappoint the audience.
You could look into Freya from FFIX or Yuffie from FFVII and I wish I could give you better examples of respected "ugly" female video game characters but they just usually tend to be male or masculine ones. Still any character can win the player on their side with virtues like strength, honor, courage, persistence, justice for example. From the summary you wrote on your character it sounds like you could do well with just brute strength, but I hope you show a flicker of sensitive side as well even if you hide it somewhere really deep.
I actually ended up looking up "tomboy characters" and this list is one of the things that came up: http://en.wikipedia.org/wiki/List_of_tomboys_in_fiction It isn't what the issue is about but still you could maybe look into some of the characters and for examples at how the author makes the audience like the characters despite the looks.
Writing a sex bomb super soldier like Lara Croft or Solid Snake is easy although I'm not saying these examples are the most shallow ones around. But writing a character without such an obvious shortcut does require a lot of writing to get the depth into it because that is where the beauty lies.