The best thing you can do is give her space, be her friend and allow her to find herself. The reality is she sounds like she is confused on who she is and is confusing that with who she "wants to be" This is pretty common in people who have lived one lifestyle for a long period of time and then learns or accepts they may be something else. This can be very confusing, frighting and even traumatic so the last thing you want to do is pressure her one way or the other.
Only she can accept who she is, and until she learns that who she is and who she wants to be is two different things she is going to struggle in any relationship wither that be with a man or a women. Some people find the change in lifestyle to be libertating and almost like a freedom of what they forced themselves to be, others find it confusing since they still "want" to be what they think is "normal" in society. Until she learns that she can still have the security in your relationship she is going to visualize security as "with a man". The good news is while this may be hard for you, if you really care for her and want what is best for her she will accept who she really is and make that choice.
I would suggest that you give her space, be her friend and encourage her to consider therapy with a therapist that is familiar with these issues. (The last thing you want is her to speak with someone who is hung up in "society's views of normal") A good therapist will help her learn and accept who she is and separate that from what she thinks she should be.
If you want to discuss this further please let me know.