Obligatory Monty Python link
I am mystified by the whole, "somebody might read this and change their views!!" hysteria. Isn't that the POINT of books? Isn't that what makes them good in the first place?
For the record
1. I have read the Harry Potter and the Narnia novels, along with several hundred other fantasy novels with countless Christian and pagan allusions, motifs, themes... I've even read all of Orson Scott Card's Mormon propaganda books.
2. I am not a witch, nor have I ever been one.
3. I am not a Christian, nor have I ever been one.
4. Neither series is even making even a vague attempt to convert anybody to a new way of thinking. They're just stories that have borrewed ideas and made allusions to other works.
5. Pullman's series starting with "The Golden Compass" should be far more controversial, because it at least actually does portray Christianity in a negative light. While not quite as fun to read as the Harry Potter novels, it has far more substance to it.
If you actually want to read sci-fi/fantasy that could challenge your views:
Farenheit 451 by Ray Bradbury
A Clockwork Orange by Anthony Burgess
The Forever War by Joe Haldeman
Stranger in a Strange Land by Robert Heinlein
The Moon is a Harsh Mistress by Robert Heinlein
Starship Troopers by Robert Heinlein
Job: A Comedy of Justice by Robert Heinlein
Brave New World by Aldous Huxley
1984 by George Orwell
The Fountainhead by Ayn Rand
Atlas Shrugged by Ayn Rand
The Satanic Verses by Salman Rushdie
Lord of Light by Roger Zelazny
This Immortal by Roger Zelazny
Slaughterhouse Five by Kurt Vonnegut
And yes, I left one out on purpose. Not trying to start a flamewar :-)