Cillian Murphy signed a contract for two movies w/ a third as an option. He will more than likely play a minor role in this film, like you stated. It should be noted, however, that Scarecrow and Joker cut a deal to work with each other to bring Batman down in one of the older novels. In "The Long Halloween", Carmine Falcone enlists Poison Ivy, The Riddler, Scarecrow, and the Mad Hatter to take down Batman. These are all characters I'm sure they're considering for the next film. Penguin is too outlandish to fit into the realistic qualities of the new Batman flicks.