[nitpick]Having read this GN, I'm not sure this constitutes an Elseworlds story. First, it wasn't marketed as such. Second, it takes place in neither a world noticeably different from the usual post-Crisis DCU (as in JLA: The Nail), nor in the past or future of that world (e.g. Generations), nor a combination of the two (e.g. The Batman of Arkham). Rather, Joker is a self-contained tale that could conceivably take place within normal DCU continuity (or what's left of it), much like the standalone Devil's Advocate.[/nitpick]
Crying Joker: Although we're not specifically told why he's crying, I took it as indicating his sense of betrayal over his criminal colleagues muscling in on his turf while he was in Arkham. Or perhaps just of the stress he was experiencing, trying to get back what was "his." Does it make him more "human?" Only inasmuch as he is a human being anyway (albeit a horrible one) and crying, like laughing, is something humans do. Going by my hunch as to why he's crying, it certainly doesn't make me feel sorry for him within this story. (As opposed to, say, the end of TKJ, or especially Going Sane, where I did actually feel bad for the bastard.)
Rapist Joker: Yeah, there were definitely other possible ways for ol' Jonny to realize that his hero was in fact a monster undeserving of adoration. Not because, as some have argued with reference to the controversial TKJ scene, the Joker is asexual. He may well be so as normally portrayed, but in Azzarello's novel there's definitely a sexual element in his relationship with Harley.