I tend to take everyone out by non-lethal means (usually stealth, breach protocol, contagion and short circuit or punchy punch time) then when I go to loot them I'll shoot them in the head. Then I pick up the bodies and dump them for more stealth XP.
I think when I replay the game I'll just give myself a bunch of skill progression shards so I don't have to play so oddly just to level up my skills.