This is another death-borg here and I did feel that about 90% of the injuries/deaths were basically asked for by the crew.
Since Security wasn't incredibly active there were a bunch of people who shouldn't really be involved like Cargo personnel in Ripleys trying to break into the AI core (and then one of the comments said something about Engineers attacking us) and so it was fairly justified. I really tried not to kill people even when lethal force was authorized, I tried to stun/cuff/RP as much as possible. I believe I'm the one who said something like "Sorry" to the poor girl who walked into R&D after we got the order to exterminate all crew within R&D and I felt really really bad for her. We only ever got execution orders for people breaking into the AI core, people in R&D, and people in areas by Genetics (And even then we didn't kill anyone until a mob showed up.)
Also, power was failing (Maybe all of the Engineers suicided against us?) and there was disorder in other places that had nothing to do with us, I still don't know what happened elsewhere but it was very very chaotic.