I'm very sorry to hear, Cerby. It's never easy watching the person you love walk away and not really knowing why.
It could just be that she's upset with her own direction and her own life at this time (I think you said she's done this before?) I feel like maybe you should just reach out to her in a few days and let her know that you're there to support her and that running away from a relationship isn't going to solve whatever issues she's going through.
I only say this because I've done it myself. Walked away from something completely amazing thinking that it was for the best and that it was what was making me miserable, when in fact, it was just myself. I will regret that for the rest of my life, I think, but I did learn from it and learned how to recognize when a problem is me or another person. I also think that if he had stuck around a bit longer, I might have realized it sooner than I did- when it was too late to mend what I had broken.
Considering she just up and left without any real reason behind it, I feel like this might be the case and I don't think you ought to throw in the towel just yet on her. It's really easy to give up on someone when you're hurt, but since you still don't really know the cause, try not to let it get to you so much and focus on trying to be supportive of her- at least for a little while. Obviously, you can't wait around forever, but given all the time you've spent with her, I think a little bit more couldn't hurt anything.
The fact that you barely fight is worrisome as well. Is she maybe the type that just holds everything inside? Never really complains? She's always the one helping other people? I don't know anything about your relationship, but I find the whole thing bizarre and I don't think it has as much to do with you as you might think it does.
Please keep us posted! I really hope that you two can work it all out- her crying and being so upset is a clear indication that she loves you more than anything, so I feel like it really IS her (lamest excuse in the book, I know!) Best of luck to you both, and my sincere advice is to not give up on her just yet x