"The Witch" is a dark comedy. It has elements of something sinister but it is also funny. It shows that the boy (and children in general) is innocent but also morbid. When parents say that their children are generally good but at times can terrorize them, no one really disagrees with this. In this story, it seems like Johnny has adopted some evil man's persona. And this all seems morbid and evil. But Johnny is just using his imagination. And in this respect, he's no more evil or dangerous that any other child who is generally good but has moments of mischief.
But even though the boy and the man both seem to be kidding, the reader is left with a residual uncomfortable feeling. Following the story, the reader might wonder about whether the man was actually kidding. Did he really kill his sister? If so, this might symbolically suggest that the adult world really is capable of evil whereas children (Johnny) only consider such evil things in an imaginative state. And if the man was telling the truth, was he successful in corrupting a young mind? In the initial comedic interpretation of the story, the man is kidding. But if he was serious, then the story leans toward a mood more dark than comedic. Jackson leaves this for the reader to decide.