I think that witches and wizards and fairies are all part of being a kid. I would also say that a lot of fantasy is based on a strong sense of good/bad, light/dark with a strong morality. How do you feel about other kids' books that portray magic or sorcery? Or about comics like Wendy the good little witch, or TV shows like Sabrina? In addition, what about Cinderella, Alladin or Little Mermaid? Or any other fairy-tales where a little magic is involved?
One one the saner Christian reviews of the Harry Potter books pointed out that what the Bible condemns is specifically the magic of dealing with otherworldly spirits - and there is none of that in the Harry Potter books.
A lot of kids' (and grownups) fantasy also deals with the misuse/abuse of power with the fantasy setting being allegorical. Pretty much inline with traditional fairy tales, Red-Riding Hood was a way to teach kids about 'stranger danger', for example.
The series is targeted at 9-12 year olds and I think that all children have some understanding from this early age that stories are not real, obviously that understanding increases as they get older.
By the way, I intend to bring up child up to form her own views - in fact I am an aetheist yet I am currently sending my daughter to a church school as the general level of education is better than the other local school.
I am happy that she will make up her own mind about religion, indeed if she decides to believe in God then we'll just have lots of interesting discussions.