I vaguely remember doing a self-challenge pacifist run... I think I had to move all the unconscious bodies on the PCRS Wall Cloud up to the dock, because otherwise, I would be indirectly responsible if it sank while they were unable to evacuate.
There is not a big difference between unconscious bodies and dead bodies in the game, after all, they never wake up. The real challenge is playing without harming anybody, which is possible up to one or two specific situations.
Or were there unconscious bodies on the ship from before your arrival? I do not remember that anymore.
Sure, I've done at least a dozen of less-violent runs (being addicted to this game and a couple of others), but you still can't get though it without ever killing anyone, at least not without hacks exploiting NPC pathfinding bugs, and the game still treats characters like Anna as dead even if you work around it.
100% of regular NPCs can be spared IIRC.