This is surprisingly easier than it sounds, as you have a counter for each chapter (and the city) for various actions completed throughout each respective area. With the chapters you can replay them and in essence reset your count if you accidentally off some bastard for getting in your way, but the city is impossible to reverse that damage, so try to avoid doing so. I would recommend not doing side missions and just running through most of the main story to make this as easy as possible. And no the knockout in the prologue does not count because it is mandatory that you knock out that guard. And when you confront the thief taker general, just leave, as the life lesson you teach him is killing him. So just avoid him, Garrett even mentions that to himself that you can just leave. So listen to the thief who keeps himself company.