No, you are not. The Strega Nona series of books, written by Tomie dePaola, have indeed been challenged because of the storyline, which is that of a loveable town witch named Strega Nona who everyone turns to in their time of need.
In the first book, which was published in 1975, Strega Nona helps people with ailments such as headaches and warts, but when she decides she's getting too old, she hires an assistant named Big Anthony. The problem with Big Anthony is that he didn't like to pay attention and missed part of a spell that resulted in his making an exorbitant amount of pasta out of the "magic pasta pot" that he is then made to eat as a punishment.
Ten other books quickly followed and the series was rated as one of the top 100 picture books of all time in poll conducted by School Library Journal.
DePaola has either written or illustrated about 200 books in his career, such as his Mother Goose collection, and numerous religious books based on the lives of the saints.
However, his Strega Nona books made the list of the most frequently challenged or banned picture books between 1990-2000 because of their "supernatural content" so you are not being any more scrupulous than alot of other people have been about the content of these books.
Michael O'Brien, author of Harry Potter and the Paganization of Culture, explains that the problem is not so much that magic is present in a book, but how the magic is presented.
For instance, the Potter books use magic in a way that turns the moral order on its head with grave distortions of good and evil. For instance, so-called “black” and “white” magic (a distinction that does not exist) is used by both good and bad characters in the book. This makes magic morally neutral, taking it out of the moral realm completely and making it into a kind of tool.
Contrast this with Christian fantasy, such as The Chronicles of Narnia and the Lord of the Rings. The difference is that magic is presented in proper context and without upturning the moral order. As O’Brien explains, throughout Lewis’ fiction, witches are portrayed in classic terms, as malevolent, manipulative and deceiving. An example would be the witch in The Silver Chair who mesmerizes the children to convince them that there is no sun. But one character, the Marsh-wiggle, deliberately burns himself in the fireplace to shock his mind back to reality. When he snaps out of it, he confronts the witch who then reveals her true nature by turning into a serpent, thus alerting the children to their peril.
When you read Strega Nona, do so through this lens and then determine if it's something you're comfortable with. If not, go with your instincts and find something else.
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