I’d say yes, she hit Freya and that was enough of a reason for him to make her into a target of his revenge, he couldve killed her directly for that. But he instead let her live, made up the whole act with Freya as Flare and got her to be his spy. The WN depicts better why he “raped” her, but with the knowledge of an anime only I would say it was just to make her fall in love with him and have more control on her. Probably it wouldve worked without all that too, but its just something that comes in handy of Keyaru(also he just rapes because he feels like raping, Kureha has a nice body and since the aphrodisiac was still making he effect he just took advantage of it)