I think they will be allies, but again, I must nerdly point to the "batman lore" if you will. I don't even have to go there though, it's luring in the background in the first film as well that Dr. Crane, beyond using his knowledge of fear as a weapon he is very intrigued by the brain and its power over the body. Obsessively, I imagine him being very intrigued by the Joker's chaotic and illogical mind. The Joker basically never makes sense, when you expect him to be scared he's laughing his ass off, so you see the dots I'm trying to connect? It makes sense for Scarecrow to work with the Joker, but I can just imagine that he either tries the gas on him as some experiment for his own interest, or that he tries to overthrow the Joker by using the gas. (Or as part of some larger scam to try and get in with Batman, that could potentially become a plot in the third movie.)
Edit: Another thing I can imagine is this. If you haven't seen the two trailers and the first six minutes, don't read on. In the first trailer, Alfred goes "and in their desperation, they turned to a man they didn't fully understand", talking about the mafia listening to, and going along with the Joker's plans. I'm guessing the Joker presents a rather simple plan (trailer 2, "it's simple - kill the batman"). In the six minute scene that was put out, the Joker is robbing the mafia bank. I'm guessing he does a lot of very bold shit, proving he's one to listen to, then gets them all to go along with him. Then, throughout the movie, his simple plan unfolds in a way the mafia didn't expect. I think the Joker is just using them. In this larger scheme of things I can imagine that Dr. Crane, who worked with Falcone, maybe works with the mob to stop the Joker with his fear gas.
