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.
I choose to believe that whomever Paul defends himself from is not-my-fault as I hide inside the Covert Closet. (Though speed-running out the front is fine too.)
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.
My memory is hazy--a decade or more will do that--but I have this picture in my head of using the Pepper Spray (which temporarily neutralizes enemies without knocking them out) on the Wall Cloud crew inside the helicopter room control deck, so that I could get past them to some necessary switch or terminal.
It might be the "carry everyone to shore" thing was on a different playthrough...