You can get rid of all human enemies by knocking them unconscious (I play expert mostly so killing is forbidden anyway). But right, if you go rambo even on lower difficulty levels, you'll most likely get overwhelmed

For the rest, you're limited by supplies you buy or find but I believe it's possible to clear mostly everything if you don't miss. I know because I found myself running around the entire map to find the remaining 1% of the loot goal