Can you use the non-CD music on the GOG version of Dark Sun 2?

Unfortunately no. The GoG version is the CD version, and you can not change the music to Midi/OPL/Adlib in its sound config. The floppy version is not included in Extras and not easy to find anywhere it would appear.
There is some mention of running an old patch on the newer version included on the CD version may work. But that is not something I am going to get into here, nor am I going to test it. It can potentially break the game at any point without knowing where or when it will break. Though the game is quite buggy anyways... so... yeah.
CD Audio is what you get.
(May look into this further if I have time, but unlikely to change outcome)

Thanks for the thorough answer! I don't mind the CD music, but it seems that as it's based on tracks it will play a track and then just be silent, where as the synth-based ones I would expect to loop more readily. I don't suppose there is a fix for that?

Sorry, no fix that I know of.

Addendum:
I looked at the SOUND.CFG for both the CD version and the floppy version. There is literally one byte difference.
Unfortunately, using the floppy config on the CD version makes the game start with no music at all. I suspect the sound code for all this is in the dsun.exe file and since I am no hacker nor a real programmer there is no way to get midi/adlib music to work on the CD version.