What killed my bunny ? (Graphic content warning)

I would suggest that your rabbit was killed by something domestic like a dog. What in nature would kill a prey animal, take its head and leave the body (where the nutrition is). Coyotes would eat the carcass unless it could break the skull to eat the brains. Wild animals kill to eat or defend themselves, something that we bred out of domestic dogs so they wouldn't eat our food unless we chose to give it to them.