After three months of dating is when the feelings are usually the strongest. If she doesn't know that she wants to be with you at this point, then she probably never will. It's not fair of her to ask you to wait for her while she is only a friend to you. I think you did the right thing. If you're not happy being her friend, there is no reason for you to continue seeing her. This way you can move on.
She is sad because she feels as though she got rejected. Everybody always wants to feel desired. She rejected you first though, so you shouldn't feel bad about this.
Don't worry about whether you will get an apology. She was confused. She is probably young and inexperienced as well. These things happen. Just put it behind you and move forward with your life.
“This planet has - or rather had - a problem, which was this: most of the people living on it were unhappy for pretty much of the time. Many solutions were suggested for this problem, but most of these were largely concerned with the movement of small green pieces of paper, which was odd because on the whole it wasn't the small green pieces of paper that were unhappy.” ― Douglas Adams, The Hitchhiker's Guide to the Galaxy