That's a shame. Are you sure the muscovy killed the dead duckling? Sometimes when animals have deformed/dead young they will eat them or fling them from the nest to avoid attracting predators.
Sometimes ducks do this, muscovys are the most common breed to do it. I'm not sure what causes it.
Put some fake eggs around the coop, Leave some in the open, but bury some in shaving/sand halfway so it looks like a nest and see what she does. If she goes to peck at it, you'll know she's...