Modern technology allows people to change genders medically and is always a touchy subject.
God does not make mistakes and allows your friend the freedom of choice to either cope with her situation and be miserable or change gender and be happy. Her path will be alot different than most of ours and will fit in God's plan eventually.
I would not worry about it too much, it is not your place to judge (like you said). Maybe through this hardship she will develop a greater and deeper relationship with God.
Be supportive and pray for her