It seemed pretty apparent through the film that the friendship between Xavier and Raven is a tiny bit strained because they are different. She has to hide, he doesn't. He cares, but he doesn't really understand.
As she grows up, and becomes a teenager obsessed with appearance and sexuality and feeling attractive and feeling wanted and fitting in, the gap between them grows wider.
Magneto encourages her to be true to herself, with the scene where she is giving blood, with the scene with the weight-lifting bar and with the bedroom scene she has with Erik. She decided to be 'free' and, seeing how humans turn on them, she makes her choice to side with Erik and not stay with Charles.
It was done in a heartbreaking manner, not a callous one. It was a touching moment. At the time she and Magneto and the others left, they didn't know Charles was paralysed, just that he was injured. And he encouraged her to go with Magneto, he told her it was what she should do.
I'm not sure why you are seeing things that aren't there and not seeing the things that are there!