What's the difference between an NPC and a CMDR? What do they have in common? Human body can not survive FTL travel without heavy protection, people still travel in Generation ships in stasis chambers (also known as Escape Pods).
Humanity failed to create fully functional AI, they end up with "bots" that can perform relatively simple tasks like hauling, mining, building, stealing. These bots build new bases while humans travel in their sleep.
But what is CMDR? Is it short for Commander? No. It stands for Consciousness Matrix Digitalized Representation. Neural copy of Commander Jameson, the only human who tried to use Thargoid hyperspace technology and died.
When CMDR's ship being destroyed 60000 Lys away from habitable space, he's just restored from GalNet backup.
Bot technology available to everyone, and different groups of people (powers, superpowers, minor factions) your them for various tasks. CMDRs does not obey anyone and act as mercenaries.
So, it is OK to destroy bots if that helps a faction you sympathize at the moment, but would you destroy someone who is technically yourself (other CMDR)?