"Okay, I couldn't figure out how to tell UFO:ET to load files on disk first, so I came up with an alternative solution (since it does load them, after files in archives). I decided to go with the route of making a dummy blank.xbig (that is, an xbig archive with no files in it). Then you can just extract the system.xbig (or whichever one you want) and replace it with the blank one, since some xbigs are outright required and the game won't start without them.
So, my suggested steps:
a) Copy 'data' directory to another place (for backup purposes).
b) Use xbig to extract system.xbig ('xbig.exe e system.xbig'). xbig is a console application, so you will need to run it from a console (obviously).