The Nemoidians are doing something much bigger than blocking a trade route -- they are playing with Galactic history.
I think this theme fits that music.
So as we build the awareness within Qui Gonn that his distrust of the council is well-founded -- that something big is up and only he seems to be aware of it -- that the boy is the chosen one and that Maul, the TF, the Queen, and the Jedi all have roles and mistakes to make in order for the prophecy to become real -- the theme should build until the final battle where the prophecy is held in the balance -- and Qui Gonn's death makes it possible for Anakin to be taken as a Padawan.
I'd like something mysterious and powerful for Jar Jar and the Gungan -- they are the only ones besides Qui Gonn who sees the age of Prophecy coming.