wow, what a rough situation. It sounds to me like a lot of this is out of your hands. I am not really sure what you are looking for, so I will just throw a couple of thoughts out there.

First of all, its great for you to be there for your friend. It sounds like she is going through a lot of emotional pain/pressure right now as she tries to be strong for her boyfriend and needs someone to help her stay strong. It is important to realize however that people often seek out support in times of need and it is confused with love/desire. She needs strength and you are offering that to her through comfort. Give her space to figure out what she wants in a relationship apart from that.

Second of all, time is a great miracle worker. You have to let her take the  time to figure out what she wants and try to move things forward. it is hard for people in these situations to move on, and so you need to brace yourself for the reality that she may never be ready to make the break. If that is the case, you need to decide how that is going to affect things.

I am sorry for everything you guys are going through. I hope that it gets better.

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Do not abandon yourselves to despair.
We are the Easter people and hallelujah is our song.

Pope John Paul II