That's some interesting trivia, Ash; I certainly wasn't aware of that. However, based on what Trooper said:

Obi-Wan and Anakin enter the room. (first three notes of Space Odyssey theme).

Dooku turns to face them (the two dramatic chords following).

I'm guessing he's going with the famous fanfare.

Also, I'm assuming everyone here has seen the Revenge of the Sith trailer, in which force lighting is shown, well, in full force. So it IS going to be in the saga before RotJ, like it or not, and the way things are set-up in the film it's going to be pretty much impossible to edit out. Therefore, focusing so much on removing it from Episode 2 to 'save' it for RotJ is futile.