I haven't taked a gun out and shot anyone other than a target throught my whole playthrough yet. I've mainly been choking out guards and hiding them to not take a big hit on the score. If you get spotted or go for a run and gun you have virtually have no chance of completing the level and you'll end it with a minus score if you do.
There is one bit in the Dexter Manufacturing level where you get a silenced sniper rifle and a hint shows a snipers perch from where you can take out a bunch of guards on a bridge but as soon as you try this your score bombs with each kill.
PSN ID: To_Many_Rules