Maybe I'm biased, but I'd be a bit disappointed if they killed off Scarecrow in TDK. I realise that the Joker is meant to be the most significant villain in said film but, frankly, I thought that Murphy was the best thing about Begins, and one of the best on-screen villains I've ever seen.
What I'd ideally like to see is both Scarecrow and Joker in Arkham at the end of TDK, only for them both to escape in the third and final film during some sort of mass-breakout orchestrated by Two-Face. Then the franchise would reach a truly chaotic conclusion with all of the lunatics running amock at the same time.