I managed to get the game to load to the main menu without crashing, and then i was able to exit cleanly to generate a settings.txt file. Then i opened the file and changed it so it read
MasterVolume=0
EffectsVolume=0
InterfaceVolume=0
After that I tried booting into the game again, and it doesn't seem as though changing those settings had any effect on the audio in the game. However, I was able to start a new game in Bounty Hunter mode, I added a single small laser onto my ship, and then as soon as I began travelling, it crashed. Here's the log for that:
EDIT: Upon reading through the log, it shows all of the volumes still being set to 1, but the settings interface in the game showed them both at the left end of the bar, even though sound was still playing. So it seems like the settings.txt file isn't even being read by the game when it launches from Wine.