Ady, could you not simply loop the score in places? Perhaps insert silences to stretch out the running time? In terms of looping the music, I'm thinking something along the lines of the background music in the game Dark Forces - it's a fairly continuous loop of OT music, some of which I believe is from the Death Star battle sequence.

As big a fan as I am of John Williams, and as much as I agree the score is a huge part of the film, I personally would like to see the clip left in. Perhaps I don't fully understand the problem, though...