First off: I agree with everybody who favors subtlety in introducing the coin in TDK.
Second: I haven't read "Eye of The Beholder" (that's the Annual, with Two Face on the cover, right?), so if what I'm about to mention is addressed there, then I apologize.
Anyway, the more I think about Harvey the more reluctant I think he should be to work with Batman. As a Prosecutor he's part of a larger justice system and took vows to uphold the Constitution. In working with Batman he's--to a degree--admitting that the system he has invested his life into doesn't work (i.e. If police and prosecution could get the job done, there'd be no need for Batman). He's also violating a lot of Constitutionally-protected liberties in the process. That'd be a pretty harsh realization for anybody to handle.
It seems to me like you could say that the first step in his descent into Two Face would be when he agreed to work with a vigilante. The next step, his scarring, obviously is a much larger part of that descent, but I hope they show some real reservation in Dent initially, and it wouldn't take too much screen time. And the coin could play into this pretty nicely: Maybe when he's anxious about meeting Batman on the rooftop he could be flipping the coin as a kind of nervous tic.