"Yeah, but I imagine it'd be difficult to make rape funny."
And that's what Joker tries to do. I think it's more akin to the TDK interpetation--he finds anything that "normal" people find horrible, like murder, racism and, yes, rape, funny and fucks with people until they get the joke.
As for how the rape case would be "funny" to him? If I read the description right (haven't read it yet, but it's on the to-buy list), Johnny was hiding from Joker that he has a wife, probably to protect her from reprisials if the police find out about her as an accomplise or, even worse, if he knew about her.
When one thinks of marriage, one thinks of it as a sort-of exclusive partnership. Johnny not telling her about working with The Joker breaches the trust in the partnership, so when Joker finds out about it, he breaches the exclusivity of the partnership by force. Not a good joke, but then again, neither is turning into a supervillain after your life crumbles around you and your body is permenately fucked up, for example.