I'm fine with thrown rocks being potentially lethal to a humanoid. There's a reason stoning was (and in some nasty places, still is) a method of execution. Thrown pebbles, not so much, unless you're adding a sling, slingshot, or other such force multiplier to the equation.
I suppose it makes some sense if there's no air resistance in the calculation as people have said. Light objects would lose more inertia to air resistance, so without it a pebble would be more like a bullet. Tumbling comes to mind as another aspect, thinking about the bullet comparison. Modern firearms use rifling to spin the bullet and gyroscopically stabilize it. Fletching does the same for arrows and bolts. Without that sort of stability, accuracy would probably be the factor to suffer the most with light throwing ammo.
As for the skull being jammed through the brain, I tend to envision that as a fractured skull fragment being forced into the brain, but that's my human rationalization. To the code and the raws, they're probably just interchangeable layers.
One thing I think should get added sooner or later: Helmets with visors and other face guards. Though I wonder if that might make things a little too easy for dwarves in full candy armor. Still, there are ways to kill dwarves without involving armor.