If you had no other mods installed in CustomAssets before and hadn't made your own changes there, you can simply rename
My Documents\My Games\Beyond the Sword\CustomAssets
to something else (CustomAssetsRemoved). I say rename in case you forgot about something that you added. If you're sure BUG was the only thing you added to BtS, you can delete the folder.
Unfortunately, since BUG and some other projects like BlueMarble all put files into CustomAssets, sometimes overwriting each others' files, it's not possible to provide a simple uninstaller.