I’ve continued to mess around with the triggers, auto-saves, and cutscenes of the single player campaign and was able to discover how to permanently destroy Rachel S’Jet. So far this is only possible on the final mission Khar-Toba. It is possible on that mission because the game creates an auto-save before a cutscene, instead of after the cutscene. Khar-Toba is the only mission where this is the case I believe.
If you destroy Rachel S’Jet just as the game creates an auto-save just before a cutscene, then load the auto-save, you will load back into that mission with Rachel being destroyed and the game will continue as normal. Once you complete the mission some weird things happen. Check it out in the video I made showcasing this glitch.
It’s kinda hard to pull off on your own and it doesn’t provide any real benefits unless you like extra challenges. This bug could be patched quite easily by just changing the time in the mission when an auto-save is created.