I've read that killing more NPCs and leaving the bodies in plain sight increases your overall chaos level. Since Shadow kill leaves no bodies behind (at max level), does that lower your chaos score? Reading around the net I can't seem to find a straight answer.
If you want to kill and still would like to see good ending shadow kill is a right answer.
I sneaked through the first mission (until you get your powers) and then killed everyone (except mission targets - for those I went non-lethal way. Yes I even spared Daud) and still got the happy "golden age" ending.
As long as you keep your kills stealthy and no one sees you kill or sees the disappearing body of an enemy (if you shoot him with crossbow) you get low chaos and Ghost each mission. The only thing you will miss from pacifist gameplay is dealing with snoring unconscious bodies and "never killed anybody" achievement.
For the Low chaos I would recommend you to keep SK on first level. That way if the body doesn't disappear you know you screwed up :D