Wait, which one? Agnes's skull was cleaved in twain by what I'd imagine is the "real" Butcher who I'd imagine is one of our standard solid lethal ghosts. If we're to believe the recreation, ShelbyPrime and MattPrime were saved when the ghost of the Butcher's son walked her into the fire. Lee ate the magic thing and became the Butcher and she's currently alive (the sole survivor of Roanoke2.)

The witch slit her throat.

She killed herself as part of the ritual.

I think the witch killed her, either that or she ate the poison fruit also.