Then it's definitely been too long for me. I literally have the original sitting in a box somewhere in the garage. The art was incredible too.
I don't have the original sadly; I was about 5 when it released. It is however, my favorite, and has been for many years. I buy a new copy every time they re-release it. (If you have the original though, some copies have Barbara's breasts exposed and others do not; the one that was toned down seeming to hint more at assault. Take that with a grain of salt though.)
But, yea. It was left largely ambiguous, and there's evidence both ways - Joker raped someone in another comic (Jonny Frost's wife) so it's not completely out of character for him. I think that at this stage, it's largely assumed there was sexual assault, but the rape thing is more questionable.
That on top of the whole idea of wanting to break both Barbara and Jim, makes me lean towards it being true. Regardless, even a hint of it (cuz there certainly is that) would probably put it solidly in the R category.
It's also why I was super annoyed with them pulling the variant cover of Batgirl. It was spot on for the total breaking down of Barbara's body and mind in that comic. The whole "Superman wouldn't have cried over Doomsday!" Well, hey, maybe he would have if Doomsday had sexually fucking assaulted him.
People have found quotes from Moore both ways; he's been somewhat inconsistent. There was a pretty chilling quote (not confirmed) from him that said Joker did rape her, but it wasn't in any of the 3 orifices; it was in the wound. Which is all sorts of fucked up. (But explains the splash of blood on her body in the panels.)
Anyways, yea. R rating.