He says he thinks stories about witches and the like are "anti-scientific", which in the strictest sense I guess they are as they certainly aren't "scientific", and that he has often wondered whether they have a "negative effect" on children. He hasn't said he thinks they have a negative effect, just that he would like to look into it:
"The book I write next year will be a children's book on how to think about the world, science thinking contrasted with mythical thinking. I haven't read Harry Potter, I have read Pullman who is the other leading children's author that one might mention and I love his books. I don't know what to think about magic and fairy tales."
"I think it is anti-scientific – whether that has a pernicious effect, I don't know. I think looking back to my own childhood, the fact that so many of the stories I read allowed the possibility of frogs turning into princes, whether that has a sort of insidious affect on rationality, I'm not sure. Perhaps it's something for research."
See, he's hardly denouncing JK Rowling and all her works. He's merely saying he's interesting in something and might cover it in his next book. You could maybe say he's reading a bit too much into it, and that we shouldn't spoil the magic for children by insisting on rationalism at all times, but to say he's been suggesting myths and fairytales should be placed on the top shelf out of the reach of kids would be misleading to say the least.
This is the same man who made a guest appearance in Doctor Who, after all.