There is probably more than one way to do it, but the only way I know of is to [start highlighting here] make stew using three black herbs and force the villager to eat it 5 or 6 times until he dies.[end highlighting here]. Although they are only pixels, it is easy to grow attached to them, and killing them does seem wrong. I have felt very bad when villagers I became attached to, who worked hard and were instrumental in solving many puzzles, eventually died of old age before they could rest and enjoy the village after everything was completed.