It was a tone issue.
She walked over to him and he admitted that he was reading her mind....and even admitted that he had many other things to apologize for (again, this is my memory of the scene, if he didnt word it that way, please correct me)... she could have...and in fact possibly should have realized/wrongly thought that he was in her mind all those years and never eased her mind, never gave her comfort or eased her self esteem issues...a typical girl of the age she is supposed to be would likely angrily storm off.
She said "You promissed me you wouldn't read my mind" and Charles said "I promissed you many things." - or something similar. I don't remember him ever saying "I apologize", but maybe I'm wrong. I'll have to watch the movie again.
I think it's wrong to mix the Charles of First Class with the Charles who can be manipulative, even a prick, which has been happening for sometime now in the comics. It's quite clear - unless I saw a totally different movie - that FC Charles is maybe näive and a bit arrogant, but he had a good heart and cared for his friends in a selfless way. He put his life in danger for Erik quite a few times - and not because he thought that he could use Erik to obtain some kind of advantage. Unlike Erik himself, btw.
So, it makes it really hard to believe that he had been manipulating and using Raven all those years. Unless the filmmakers decide to show a shady side of Xavier in the next film, which would certainly disappoint me. It seems that it's cool these days for a fictional character to be manipulative, shady or just plain mean. I very much prefer the FC version of a näive, idealist Charles who has human flaws, but would never be a prick (especially to his friends).
The way it was portrayed was one of old loving friends parting and being sad about it. Not sure that was the best choice for clarity...even though i still found it clear.
The way it was showed in the film...Raven seemed to care about Charles, and then just left him there. Following her through the film, even if she was mad with him for not helping her with her appearence issues, the way she abandoned him was just awful - she really seemed to suddenly turn into a totally different character.
Like I said many times, I can totally understand her leaving him to be with Erik, but not at
that moment, the worst moment in Charles' life. The same goes to Erik btw, but at least he hadn't known Charles since they were kids.