^Exactly the same thing happened to me in Deus Ex.
It was that mission which had you steal, if I recall right, a vat of ambrosia from a chinese ship, which was docked on wharfes. Just like with any mission in DE, there wasn't really a point in killing people; the only guys you could call "evil" were the Majestic 12-thugs and I avoided killing even them. Basically, the only thing I disabled was bots and those commandos; they had lost their humanity already, willingly. Killing felt justified to me.
How does this all matter when the ship level was strictly a non-MJ12 mission then? Well, from time to time I screwed up, trying to play the perfect ghost, kill no one and only KO people when necessary. Sneaking, invisibility, using vents for travel, etc. It didn't always work out right in the end. I ended up killing some of the crew in that mission, purely out of being too hasty. I should have taken my time and sneaked better, but I wanted to advance. Later, when I searched through the ship logs and registers for codes and the odd email, I came up to this message which was send to a ship officer. Nothing odd in that, just that it came from his relative and it talked about how his son was doing in school, how they wanted dad to come back soon, etc.
You could say I felt quite bad afterwards. And there were no loads from before my run in with the crew in the lower levels of the ship. *sigh*
Who said I can't post long ones?