The original loose plan was to extend Harvey's story into the third where he would become Two Face in the opening scene, during Jokers trial. They decided not to go in that direction. Thank god. What a disaster would that have been if they left too many loose Joker threads and then Heath dies before they can film it?
There was no plans at all for Joker in a third movie. Of course they would have written at least one more scene with him once they started working on a third. But there's no guarantee that Nolan would have returned for a TDK sequel unless Joker fit into his "conclusion" storyline for Bruce Wayne. Nolan didn't want to do another sequel, next adventure for Batman. So I imagine Chris would have produced the next film (like his role for Man Of Steel). A new director would have used Heath, Christian etc the way he saw fit. And the story would have kept going until someone new decided to end it their way OR until the franchise ran itself into the ground once again.
The other option would have been TDKR by Nolan, just with Heath in a glorified cameo role. At least a couple of scenes, stuck in Arkham. Joker would not have had makeup on his face, that's just common sense to me. And quite frankly I think too much of that takes away the mystery surrounding his Joker. I wish Heath the man and actor was still alive and I'd be curious to see what he would bring to a sequel, but there's something bittersweet about the way Joker's story ended in TDK. I appreciate it in a weird way because it adds to the creepiness of Mr. J. I'm also satisfied with the explanation given in the official TDKR novelization.
So to sum it up, I really don't believe his role would have been big in the sequel unless a new director was on board. And I don't see TDK's ending as a setup. It's simply the thoughts of a madman before he loses to Batman and Commissioner Gordon.