The Gemini droids have a Hivemind, whenever one is destroyed it's consciousness is absorbed into it. Where it remains until a new chassis is created, now going through Chapter 4: Where Dreams Die if you do the bonus mission with the Technoliths. It's hinted by the Iokath Master Builder that Scorpio is just a Gemini with ornamental parts added on, so it got me thinking if you choose to destroy her doesn't that mean she's in the Hivemind and still be able to come back later?
Now I was thinking will she try and upload herself into Gemini Prime and cause trouble later? Though for those who chose Lightside she might recreate her body and become a companion again, i'm hoping those who choose Darkside can eventually get Gemini Prime as a companion and we get the chance to destroy Scorpio's conscious once and for all.
Although I could be overthinking things and she is dead for good, because the modifications she might of been cut off to the Hivemind and never coming back unless you chose not to destroy her.
I just remembered that if you destroy Scorpio, Vaylin has that Purifier Droid reset the Gemini Droids to default settings. So that could also mean Scorpio's conscious is reset to default and Darkside choosers, could have her back as a companion without her self-awareness.