You're being uncomfortable is understandable as you don't have romantic feelings for her. But recently you would have claimed her as your best friend.
She hasn't changed who she is at all. She opened up to you and was very vulnerable about a sensitive situation in her life. That is not always easy to do.
I suggest you reevaluate your friendship. If you actually do still care about her as a friends and have a good time when you are with her I would encourage you not to pull away from her because she will understand your pull back occurred after she opened up to you and that is sending the wrong message.
You don't want her to be fearful sharing that type of information in the future with someone else she might be close to for fear of rejection.
Get together with her and have fun with her just like you did before you knew what her stepfather did. Remember she was a victim.
You don't know that she is gay or has a crush on you if you're being honest. So, continue to see her as a friend like before but if she gets into your personal space then let her know clearly you don't like that and you're uncomfortable. If she actually does 'arrange' to have your elbow fall on her boob then pull it back quickly, make it obvious you pulling it away. If something like that does happen it is possible it was an accident. Accidental sexual touches just don't happen that often so if you experience a couple 'accidents' you can can either address it - if she's you're bestie you should be able to say something. At least then if you start to pull away she'll know it because of the 'touches' and not her opening up to you. Is it possible she isn't gay and you're misreading the situation? IF this is the case how would you feel pulling back your friendship. None of us know the situation so my advice is to continue being her friend - if she really did feel like a best friend to you - and don't jump to conclusions, let the situation play out.