Got a little workaround here:
Only use the modified upgradegenerator.lua briefly, when only the admins are around to obtain it with the dev commands, then revert to the normal upgradegenerator.lua, but keeping universalsystem.lua around. This will keep any Universal System modules you have already created, but making it unobtainable through normal means.
Probably won't stop it from dropping when your ship is destroyed but frankly, something is wrong with you if you somehow get killed while having this installed...