I used to kill things (birds and small mammals) with my BB gun and when I got older felt real bad about it. On the other hand I never flinch or get buck fever now when I squeeze the trigger!
I think its the intent. I couldn't kill or injure a critter for the sake of killing it, but I have killed dozens of lobsters and thousands of shellfish and feel absolutely no remorse. I also know of at least twice I ended up making roadkill, but It really doesn't bother me because it was the dumb critter responsible both times. One was a bird who decided it could fly through my windshield while I was driving down the highway, and the second was a squirrel who must have had something wrong with its head. It kept running back and forth across the road. The first time I passed it, I stopped and let it go by. On my way back I did the same thing, but the squirrel decided it could run between my front wheels and my back wheels. it was wrong.
In the case of the duckling, it was in the wrong place at the wrong time. -Assuming the primitive's story is true. The only way I could imagine feeling bad about it is if the primitive intentionally tossed the rock at the ducks to scare them off and miscalculated.