She allowed herself to believe it was something else because she needed something to believe in, but we, as readers, should be able to see through this. No, he didn't. Apollo forced himself on her, but he is non-sentient. Don't let Pris' desire for him to be anything else fool you. Non-sentients do not rape.
Rape is an act of violence.
What Apollo did was something else, something without shame, something natural for him. She would be hurt and fear men. The last thing she'd want is to be around him. Rape has terrible effects on the victim's psyche. No one should deny that.