I would think that some of the decision would have had to do with what was going on in the flick at the time. THe Klingon music from TMP has an action-based rythm (or is it tempo? I don't know) which lent itself well to the action of the scene. The DS9 music was a softer, slower tune which would not have worked well in that situation, IMHO.
Agree or not, more important to the filmmakers than a nod to the fans would be how well the music helped to tell the story.