"My books are about killing God.""
Yeah, but that doesn't mean he's trying to kill god in the mind of children at all, in any way. Indeed, take it in context and he's just saying that a series that involves killing God should really be getting more controversy from fundamentalists than a series about a boy wizard.
There's definitely elements of anti-organized religion in there, although I'm not sure how it instantly becomes against Catholics:
"That's not to say I disparage the religious impulse. I think the impulse is a critical part of the wonder and awe that human beings feel. What I am against is organised religion of the sort which persecutes people who don't believe. I'm against religious intolerance."
So uh... is there another quote where he explicitly says it's anti-Catholic, or is this another "I read it on some site that didn't source it and now I'm repeating it" kind of quote?
EDIT: And looking at the Narnia thing, he seems to be criticising it due to sexism and stuff rather than because of its Christian message. I mean, this quote doesn't seem particularly anti-Christianity as a whole to me (if anything it's in favour and just saying that Lewis horribly twists the message):
Pullman also makes the argument that Lewis really isn’t all that Christian. The fate of Susan Pevensie, he told me, indicates “some sort of crazed, deranged Manichaeism. Here’s a simple test: What is the greatest Christian virtue? Well, it’s charity, isn’t it? It’s love. If somebody who knew nothing about Christian doctrine, and who had been told that Lewis was a great Christian teacher, read all the way through those books, would he get that message? No.”