Are they any moments in Freespace campaigns that felt wrong or made you uncomfortable?
In the Derelict mission "The Sting", you are ordered to capture the cruiser Minerva, and they agree to surrender. But when the Auriga shows up, Command orders you to forget about capturing the Minerva and just kill them. Killing a surrendering enemy is a war crime. Sure, they did try to escape when the Auriga arrived, but they weren't even given a warning or an option to stand down again, Command just said that we had no use for them anymore, so kill them.