As far as I'm aware, no. One of the composers did post the ending cutscene music without any overlaid sound in his online portfolio which can now be found on Mojo Soundtracks
, but if I recall correctly he didn't release any more because LucasArts made him remove it roughly a day or so later. Any other releases of the music, including those included in the game itself, have the sounds unremovably overlaid directly into the mp3 files.
It's a shame too, because whilst EMI's soundtrack was certainly not as good as CMI's, it was a decent listen. The overlaid sound effects make it pretty much impossible to enjoy though since unlike with CMI, it doesn't sound like much consideration was put into making the sounds actually work with and accompany the music -- they're just 'there'.