Hmm... it makes sense if Batman is indeed portrayed in that light of a vigilante out to fighting petty criminals for his own self-indulgence (and the self-indulgence of personal loss is damning - the idea that THIS wastes your life away is a powerful and potent theme, one I'd love to see Batman considering his own 'crusade' over). It would make
TDKR a powerful commentary on batman/vigilantism/superheroes on it's own, and would really liberate it as an individual film. On the other hand it would also mean that Bruce's struggle in
Batman Begins (which was, indeed, reconciling between personal and universal 'justice') was all in vain - that he has failed in his mission to bring 'true justice' to Gotham City, that "the point of Batman" who makes the "choices no one else can make" is nothing but megalomania on Bruce Wayne's part. It makes me wonder about, and I'm sorry for this but,
Batman Forever. Bruce's line to Dick about how you wake up one day and realise that revenge has taken over your life, those were very, very potent themes, but they also solidified the idea that these heroes, in an attempt to oppose the petty criminals who have taken their lives away, had found those criminals in the supervillains that are out there (Dick's point that it was Two-Face who literally killed his folks is another debate). What that means for the Joker though is this: he corresponds to those supervillains almost as a paradigm. I'll be just as content with Bane reminding everyone of the Joker bringing anarchy to Gotham all those years ago, as a point that he was "right" in saying that the Batman is just as corrupted as he was. I wonder where Selina Kyle fits into all this. If rumours of Scarecrow making an appearance is true, then maybe he could be used as an example of the 'freaks' and have Bane solve his recurrences with a bullet.
To answer your questions: 1. The silly answer would be that Bane kills off all the freaks. :P but no, maybe the Joker isn't playing in Gotham this time around because there is no Batman for the most part? Ideally speaking, if he remains incarcerated in Arkham, it brings Batman's own conviction that "you'll be trapped in a padded cell forever" more meaning. But the irony of both those lines is that they're both true - the Joker is incarcerated in Arkham for all these years, and at the same time he is continuing his war with Batman by breaking out. I liked how in
Watchmen we saw that the villains all faded away and the good guy remained alone in the forefront. Call it a vicious cycle, but maybe that's what happens to Batman at the beginning of this film? Ultimately, however, the Joker's absence doesn't need to be explained because of his nature of being unpredictable. In other words, I really, really, don't know

You can also nullify the threat of Joker simply by making Bane a greater threat, that, at the very least, can be accomplished.
I know none of that answers your questions :P but it's fun to guess.
2. Well, for one thing he's insanity is clear and thus it makes him attempts meaningless altogether. Maybe he is content with having Batman remain the 'villain' in Gotham's eyes - it'd suit his infatuation with Batman as a symbol for Gotham's soul. I think it depends on how they explain Harvey's death -- was it because of the exploding hospital, or because of Batman? Eitherway, it is Batman's fault and this would be enough for the Joker to rest on.
I'd be content with that, but it wouldn't answer TinkerTailor's question #1.