Moore's insinuation in The Killing Joke of the Joker undressing Barbara and photographing her was that she was raped while she was bleeding from an abdominal wound. There's nothing more explicit than that insinuation. It is a very hard core story from that perspective.
I think Moore's insinuation was that it was Joker's insinuation (without actually being reality).
I just don't get the feeling that Joker's condition.....perspective...allows him anything even resembling a sex drive. I think that would involve him too much in "the joke" for his comfort.
The only wording that Moore ever used to describe Joker's assault on Barbara was "molestation". If he's gonna take the opportunity to clarify and say that it was a rape, then I imagine he'd use stronger wording than "molest". I'd say "violation" would make it more definitively a case of rape.