Vladius said:
I'd say it works better without. That music is for a scene with a much greater emotional impact. Not that Qui Gon's death is bad for it, but this is the end of one movie, not three.
I mostly agree with what you're saying. I'll probably save this music for the Anakin vs Dooku fight in Ep. III. However, a small part of me feels that Obi-Wan's "rage moment" needs more impact, so the music may make it into at least one version of my edit.