Implement a sort of plague that attacks villages, usually in form of infected animals that villagers can bring in.
Well obviously you can tell there is something wrong with the animal if it spots you and precariously follows you.
Imagine a bear going happy-go-lucky with you, following you shyingly, whilst you run away screaming. Then the group comes back and hunts it, curious to why the animal never fought back, and carried the corpse back to the village...
They skinned and butchered, then wondered why the meat was odd looking, then cooked and ate the meat.
The next day, the ones who ate the meat gets a disease called "The Plague" which lowers the speed of which your character moves, and greatly lowers your stats and skill levels, making you unable to play as your character properly. The sick character then has to be in bed, but with no cure, the other villagers slowly gets the sickness, and the village dies off.
The plague then lingers on in organic substances, like any water barrels or food the sickly touched.
Thieves then goes in and robs the place, having no idea they just picked up the plague, and boat or wilderness warp to other areas to rob more places... Thus spreading the grim disease.
How's that?
Make intelligence and perception needed for a hearthling to be a possible doctor or a witch doctor in some cases, for a village.
Don't know if a skill set will be needed so you can craft new stuff that goes along with this.
Obvious griefers is extremely possible by the way, so with this idea, what they'll just simply do is toss items into a village or give people infected items.