Jedi Knight let you select (when you first did a full install of the game) between "high res" and "low res" sound effects. This was a nice feature as the high res sounded much better.
Sadly, Mysteries of the Sith, like the JK1 demo version ONLY allowed you to use low res sounds. As a result they sound more muffled and crappy than JK1's high res. It's too bad really. I guess they did it to save disc space. :P
I once considered releasing a big goo file of the JK1 high res sound effects converted for use with MotS, but I just never had the time. I'm sure you could still do this if you own both games. It would be a big file, but perhaps worth it. Most of the stuff is the same between the games after all. The voice files would still be lower quality, but many of the sound effects would sound better.
So short of doing it yourself, no, there is no solution. MotS sound quality is just stuck in low gear.
If somebody released did convert and release it now I'm sure some fans would really appreciate it!
All you'd need would be to rename some files and use a gob/goo extractor program like ConMan (free, on the net), plus all three original CD's.