Hardly. I mean, take Tolkein for instance, while of the belief that Theology should be left to Professionals, He had deep seated Christian beliefs, however, in his masterwork, he has Wizards on both sides.....Not too much different....
I mean, at the point of the target audience, you are asking for them to be attenuated to subtleties, at a time when the generalities of good and evil should be the operative theme.
Kind of a timing thing.
let me make it plain... i think it is better, when dealing with children who are in a period of character and morality formation to have books/movies etc. that say WITCHES/OCCULT BAD, OTHER THINGS=GOOD. i think it should be that plain. i think that having witches as good protagonists muddy the waters unnecessarily. She could have had FAIRIES or ELVES as the good guys and witches as bad guys, but she didn't. why not?