Demented and powerless, the aged being could only weep and mumble in fear and pain and misery and he shrank away from what seemed like another threat . . . He was as light as paper and would have followed them anywhere, having no will of his own."

If you haven't read Philip Pullman's trilogy, His Dark Materials, you might not instantly recognise his description of The Authority - better known to most of us as God.

Pullman's Authority is "of terrifying decrepitude, of a face sunken with wrinkles, of trembling hands and a mumbling mouth and rheumy eyes" who "cackled and muttered to himself, plucking incessantly at his beard".

When a leading character, Mrs Coulter, is told that he suppressed the angels, "since he came into being", she says: "The Authority created the world. How can he have come into being?"

"There may have been a creator or there may not. We don't know," is the answer she receives.

Isn't that the only answer there is - in fact as well as fiction?

The Catholic League of America doesn't think so. It woke up to Pullman and his assertions of a false God only after his trilogy had sold 15 million copies and had been in print for 11 years. Just as the film of his first book reaches the cinema under the title, The Golden Compass, the league is calling on American parents to keep their children away from it. Quite why is puzzling.

The books may be theologically challenging but the film-makers have neutered them. They anticipated the narrow-mindedness of America's Bible belt and secularised Pullman's epic tales. These stories, written to challenge "totalitarianism from communism to theocracy" have been watered down to satisfy the requirement of that other imperative, mammon. Where Hollywood blockbusters are concerned, you don't challenge the audience. The box office take is their god.

It is disappointing to all who have loved the books for the way they brought us back to the big, timeless issues that confront mankind. Those who have religious conviction believe in a creator. Others place their faith in the Big Bang. Most of us float between the two, maybe choosing not to think about it at all - until someone like Pullman stops us in our tracks. His writing reminds us that we don't know for certain either how we got here or why we are here. In an attempt to rationalise this conundrum, mankind has produced many religions over the centuries. But we have no empirical proofs for any one of them. It's why we call them faiths, isn't it?

Yet, the stronger a religion grows, the more millions of people who willingly live by its tenets, the more the lack of scientific proof for it tends to be forgotten. We have painful examples throughout history, from the Spanish Inquisition to the Taliban in modern Afghanistan. Such is our respect for religion that, in most societies, even our secular one, we revere its lieutenants as God's representatives on Earth. Pullman's writing acts as a reminder that they are guardians of a faith, not owners of a proven truth. His books remind his readers of the preciousness of freedom of thought and the importance of fighting for it.

It is the healthiest possible reading material for children and young adults, even if his methods come as a rude awakening. When I first picked up Northern Lights (which is now filmed as The Golden Compass), I was shocked. For here was a children's book in which the source of all evil was an organisation called the Church.

It was a church peopled with priests, monks and bishops yet, almost immediately, even to someone like me, who was brought up as a Catholic, it was clear the institution in the book was not one church but all organised religion - at least all that want to control the freedom of thought of their members.

The books have excited the imagination of children and parents alike. The Archbishop of Canterbury enthused about them when he discussed them with Pullman, during the staging of His Dark Materials at the National Theatre in London. A Liberal American Catholic theologian, Donna Freitas, says the trilogy is a religious classic in which an old patriarchal model of God is killed to make way for a new divinity "fit for our age". She describes Pullman as "a reluctant theologian".

So why did the film-makers bottle it? The child characters in the book risk life itself to fight for freedom of thought. Isn't it ironic and pathetic that when the film-makers carried that challenge on to the screen, they secularised the threat? It doesn't take much of an examination of world affairs to understand that zealotry needs to be challenged.

There isn't even a strong commercial argument. The same league called on the viewing public to boycott The Da Vinci Code and the film was a box office hit. It probably factored in that these films are for children and thought they therefore required to be anodyne, inoffensive. The league should take another look at the children's stories that have lasted the test of time: Little Red Riding Hood, Hansel and Gretel, The Snow Queen. They are laced with horror, cruelty and outrage but they contain a truth.

The secularisation of His Dark Materials won't spoil the story for those who haven't read the books. There is plenty of material in a tale that follows a 12-year-old heroine on a quest to find her kidnapped friend, Roger. Her journey takes her through parallel worlds with the help of a talking, armour-clad polar bear and a flotilla of ageless witches. It's a story in which the characters have external souls, in the form of animals, called daemons.

There is enough to make three epic films that will bring children flocking to the cinemas, but this is an opportunity lost. They could and should have remained true to the books - and the religious institutions should have encouraged them. This was a golden opportunity to get children talking about theology. The books may have challenged a patriarchal God - depicted him as a pretender who had been usurped by his regent. But they do at least mention God. They also present the most spectacular images of angels. Pullman's work has been described, correctly in my view, as "an imaginative springboard for discussion that sometimes leads to embracing God". Instead, fear of censure and the imperative to make big profits have ensured it is just another secular film.

Pullman has stated that it doesn't matter to him whether people believe in God or not. He is a champion of kindness over cruelty, democracy over tyranny, open-minded inquiry over the shutting of freedom of thought and expression. He is right when he says: "To read a great story is not to absorb a doctrine but to begin an imaginative collaboration. It is that freedom that the boycotters find so frightening. Thou shalt not', is soon forgotten. Once upon a time lasts forever'."

We must hope that when children leave the cinema, they will pick up the books.