I really don't like the idea of making Joker a member a the League of Shadows...Joker is an anarchist, his disfunctional mind is his greatest weapon. Ra's is definitely dead IMO. And this twist will be too much alike the Begins twist. Sorry.
The Joker wouldn't have to be a member of the League of Shadows, per se, for this twist to work. After all, Scarecrow in
Begins wasn't a member either, but was recruited by Ra's to weaponize the hallucinogenic effects of blue poppies. Plus,
only Ra's would have known about the Joker, keeping his existence secret from the rest of the League of Shadows. Ra's probably figured that his plan to infect the city with fear gas would have worked well enough that he might not have needed the Joker, so no reason to tell his minions about him. Still, knowing full well that the economic assault on Gotham failed, he would know that there should be an alternative plan on the slim chance that this would fail as well. After all, the Joker, being insane and certainly dangerous, would be akin to a nuclear bomb as far as Ra's was concerned, strictly a last resort should the plan fail and he is killed in the process--which is exactly what happened. The Joker, being the anarchist as you said, would have loved Ra's plan of causing fear and chaos in Gotham, especially the idea of it creating a snowball effect throughout the nation. That would have been payment enough for him. When he saw it fail, no doubt he would have gleefully said, "Now it's my turn," and prepared himself to finish the job and to take down Batman in the process. Granted, it is only an idea, but it certainly do-able and logical IMO. As it being too much like the
Begins twist, remember it is a sequel and part of Batman's beginning, if you will. Why not use Ra's Al Ghul--or rather his legacy and effect on Bruce--as a connecting point? Besides, Ra's would still be dead.