I might be way off, but it sounds to me like he cheated on his girlfriend, and he feels really guilty about it. I think the 'you' is the girl he cheated with, and the 'she' is his girlfriend. He can't stop thinking about the other girl, but he wants to, because he doesn't want to hurt his girlfriend who has no idea about the whole thing. He just wishes he had never met the other girl in the first place.
I might be way off, but it sounds to me like he cheated on his girlfriend, and he feels really guilty about it. I think the 'you' is the girl he cheated with, and the 'she' is his girlfriend. He can't stop thinking about the other girl, but he wants to, because he doesn't want to hurt his girlfriend who has no idea about the whole thing. He just wishes he had never met the other girl in the first place.