Well, well! Children's literature has come far since C.S. Lewis, eh? I'd say let some people be helped but don't let them go overboard.
In an interview with Literary Review, Pullman says that The Book of Dust will contain his response to accusations that the previous three books portrayed organised religion as exclusively repressive.
“This is a big subject and I’m writing a big, big book in order to deal precisely with that question,” he tells the magazine. “I don’t want to anticipate it too much by switching a light on the answer now. The interesting – the curious – question is, if people can be helped by something that is palpably not true, is this better than denying the thing that is not true and not being helped?”
However, I will be much interested in seeing how Lyra's adventures continue but I thought that her story was pretty much at a full stop after The Amber Spyglass. But then I don't really remember the story much, having read the trilogy years ago. (I don't even remember the name of the boy from the second book.)