Well, my first concern there would be racism more than sexism, though if she's local or disassociated from the western cultural sphere then I think that won't be much of an issue.
From there I personally think the only thing that needs to be done is: avoid reliance on sexual assault or other trauma to build her strength (use other sources of psychological discomfort), avoid needlessly sexual attire (doubly because she's supposed to be 12 O_O), don't have her become too reliant on male characters (or rather, if there is a reliance, make it not overwhelmingly go one way and be more of a partnership)*, and once she's passed the terrified->capable summit, avoid making her seem pitiable if she's injured or dies. Though before that I personally think it makes in-world logical sense for her to not be a super badass, and contrasting prior vulnerability to the sort of action-survival heroine with psychological baggage she's supposed to end up as.
Of course the age makes a lot of these lesser issues in the first place since audiences will already be put off if you either sexualize or brutally murder a kid (which eliminates a lot of the vaguely sexual brutality which might receive tentative criticism). If you're really concerned I'd fly the game by people who've done gender studies or otherwise familiarized themselves with gender in media and might be better equipped to identify potential issues.
* complicated by being a young character at the start, though this could establish some of that "toughness" by having people who offer her help try using her for child-labor or otherwise abusing her in a way that doesn't rely on the first point since it is overplayed, and the point is to escape from that rut.
His premise was to set the game in Somalia or somewhere similar, a rather horrible and unequal place. Let me run through each point with regards to the setting:
Racism: I am not sure why you would be so worried about racism, since I doubt the developer was planning to make caricature black characters as in "Tintin au Congo". Such a game would not appeal to many nowadays. Why would racism be not a risk if she was "disassociated from the western cultural sphere", whatever that means? If you mean that she is a Somali, then that is of course more likely, unless she is the only white survivor of a pirate attack or something like that.
Sexual assault: Being raped does not build anyone's strength, so that is bogus anyway. Rape is common in Somalia, especially of young girls, so the character may have been raped and it is not sexist to portray it.
Needlessly sexual attire: Somali girls, being mostly Muslim, do not wear sexual attire, but if her clothing has been damaged or lost it may reveal more skin than she likes. Obviously she will not be showing off her body on purpose, and will try to find more suitable clothes if she has none, but the damage inflicted on somebody's clothing should not be affected by our squeamish morality!
Reliance on male characters: She's a 12 year old girl in a civil war. If she does not find an older, more experienced mentor, most likely but not certainly male, she will get wrecked hard, even if only by dying of thirst or hunger. Your concerns about this could be solved by making the mentor female. Obviously the partnership between a 12 year old and a 30 year old will not be equal. The mentor can be kind or abusive, but will not see a 12 year old as an equal - would you?
Terrified/capable summit: Does not exist. Experienced soldiers are still usually terrified. They just function regardless.
Avoid making pitiable in death: Anyone retching as she slowly bleeds to death from a shot in the stomach looks somewhat pitiable (see the poetry of World War 1). People do not metamorphose as they become competent warriors.
Not being a super badass: She's 12. She can be when she grows up.
Audience being put off: That audience is not ready to face the virtual horrors of civil war. Butchering and raping children is not as rare as it should be in these places, and it is possible that the hero will end up fighting other child soldiers, who may be drugged and raped by their masters. War is hell, repeat until you understand. Besides, vicious slaughter of children never put off DF players.
Gender studies: Those people would reject the nation of Somalia as sexist. They would do the same to the game. This place is close to a hellhole, so judging it by the standards of a decent society will only give a negative verdict.
If that sounded a little harsh, I am sorry.