So I shot a tranq dart into someone's head and I got the Merciful Soul bonus, but then when I go up to loot the corpse, his icon shows a skull, does that mean he's dead and I just screwed up my pacifist attempt?
It actually is a little grey here.
Sometimes the game bugs out in two different ways.
The first way is that the guy dies from the fall (of like 2 feet), which isn't supposed to ever happen.
The second way is that some people show the skull while they're actually knocked out.
It's safer to load the save again, but some people have continued on after seeing someone they knocked out with a skull and have still received the achievement.