Assuming the two mixes have the same bitrate and the same number of channels, you could do this kind of "splicing" in Womble, and export the audio to 5.1 AC3. Then, import the newly created AC3 track into Audacity 1.3 to do the music fadeout in the conference room scene. Then, making sure "use custom mix" is selected under Audacity's export preferences, it would be a simple matter of exporting to a new (presumably final) AC3. From that point, I'd recommend re-importing the video and final audio stream into womble to make sure there's no audio drift. If everything looks golden, import the streams into whatever DVD authoring software you're using (I prefer DVD-Lab Pro), insert chapter breaks, and author the DVD.

Again, it may sound complicated to the newly-initiated, but it's really quite a simple edit in theory. Of course, you'd end up with a DVD of the bare-bones video sans Adywan's awesome menus and special features, but aside from that the only loss would be the added slow-mo to Obi's death scene.