Is this guy dead?

Solution 1:

He looks dead. Normally if someone is knocked out they have a "Zzz" icon instead of the skull... you're not a pacifist. Load save.

Solution 2:

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.