He was talking about Heath and himself. He didn't refer to Two-face and the Joker as being d'accord. According to the script review, which I do trust, and my own opinions, The Joker is after Harvey as well as Batman and Gotham throughout the movie. He cracks Harvey, possibly scars him, and then after hunting him as Harvey Dent the whole movie, now, Two-Face goes after the Joker with a personal vendetta. This is much more plausible.
As, just with The Long Halloween and Dark Victory, Harvey first tries to bend the rules of the law to stop crime. Then, as Two-face, he uses killing as his method to stop the same criminals he fought while he was Dent. In Joker's words, "Two-Face is the same ol' Harv". Because as Dent he was only out to stop the mob, and as Two-Face he was only out to stop the mob.
Only now, he will be after the Joker as Dent, while still playing by the rules. Then as Two-Face he will still be after The Joker, yet playing by his own laws and regulations. This is very much more with-in Two-face's character (in current continuity) rather than teaming him up with the Joker (I can see him teaming with other villains, but Loeb created a deep hate between the Joker and Harvey in The Long Halloween and Dark Victory that I don't see them getting together. The Joker only worked with Two-face in Dark Victory because he had his own agenda and Harvey was desperate for all the people he could have on his side....but, as we saw they had no problem holding a gun to one another's heads.
I think that Two-Face will very much be at Joker's throat. And eventually Batman's, in the third picture.
-R