Now, this COULD just be a throw away line to highlight a character trait that Fett is known for BUT what if we look closer. Vader as Anakin may have known Fett in Ep. III and in fact worked with him after his fall to the dark side. Fett wants to avenge Poppa Jango's death and so he teams up with Tyrannus to help kill Jedi.
IN Ep. III we know that Mace Windu is gonna die. (GL and Jackson say so in numerous interviews on both the DVD and during the marketing blitz when AOTC first came out) We know Mace killed Jango. Hence Fett will want revenge on Mace in particular.
Now as a writer I like to examine various scenarios and this is one that comes to mind with this particular dialogue. What if Mace knows the location of Obi Wan and Yoda and where they are escaping to in the end. Mace decides to hold off the attackers, Anakin included that are storming the Jedi temple - whatever scenario you can imagine for Obi and Yoda's escape from the purge, personally I think the dramatic way to puntuate the purge's beginning in Ep. III is just to storm the Jedi temple witrh clone troopers and heavy weapons after it is discovered that the Jedi have been playing both sides against the middle and have been manipulating the whole clone war (that Palpy is a sneaky bastard

Anyway, Mace is holding the attackers off and Anakin knows that Mace knows where they're going, he wants Mace alive, but Fett disintergrates Mace in a knock down drag out fight. Fett is satisfied that he had had his revenge but Anakin is furious that he lost his only lead on where his old master and Yoda have gone.
Years later he runs across Fett again on teh Executor and admonishes Fett: "No disintergrations."
A little long winded but I could see it as a nice little payoff for the fans.
Okay, Okay I admit it, I want GL to let me at least collborate on Ep. III
