My knee-jerk reaction to this unsupported assertion was to counter it as a myth; however, I was reading Alan Garner's, The Voice That Thunders [0], this afternoon – specifically the essay, The Voice in the Shadow – and my understanding of myth has deepened; so, instead, I will suggest this assertion is a canard – and not in the sense of the lumps of sugar the French dip into their coffee.
His Dark Materials (HDM) is a retelling of Paradise Lost [1] – Milton's epic poem of the story of Adam and Eve. Its foundational myth is the keystone of much religion. Pullman is a scholar of Blake, and his grandfather was an Anglican vicar whom he was close to as a result of his father dying when he was young. Pullman knows precisely what he's doing.
Where some Christian groups – I will refrain from labelling them as fundamentalists – seem to have backed into their breeches is with Pullman's portrayal of The Magisterium (which some Catholics believe represents themselves), and that in the telling, Pullman kills God.
The Catholic church has – to say the least – had a colourful history. Much of it sanguine – in colour, that is. That's undeniable. And if a parent should want to censor their 8-14 year old reader from the harm that HDM might thrust upon them with the behaviour of The Magisterium, then they are going to have a whale of a time "protecting" them from history of the Catholic church. Good luck denying Martin Luther's place in history; let alone the Inquisition.
Before I tackle the alleged murder of God, can I point out that the Archbishop of Canterbury loves HDM [2]. This is someone who holds a role first filled by Augustine in 597. (Augustine was quite something. Do read his tale.) If anyone on the planet was going to callout Pullman on atheism, the ArchBofC was the man. Nope. Not only loved it, but recommended it.
And yet, in the US, the books were censored [3].
The most telling expurgation is this from the point of view of Father Gomez (of The Magisterium) watching Lyra (the protagonist):
"And there it was: the dark-blonde movement that was the girl's hair. He moved a little closer, and took out the rifle. There was a telescopic sight: low-powered, but beautifully made, so that looking through it was to feel your vision clarified as well as enlarged. Yes, there she was, and she paused and looked back so that he saw the expression on her face, and he could not understand how anyone so steeped in evil could look so radiant with hope and happiness."
"... he could not understand how anyone so steeped in evil could look so radiant with hope and happiness."
For me, in context, this one of the most beautiful parts in the trilogy, but in the US – the Land of the Free, the bastion of free speech – you cannot read it.
God, of course, is not murdered in HDM. First, let us see how Pullman describes the place of God in his universe:
Balthamos (an angel) said quietly, “The Authority, God, the Creator, the Lord, Yahweh, El, Adonai, the King, the Father, the Almighty — those were all names he gave himself. He was never the creator. He was an angel like ourselves — the first angel, true, the most powerful, but he was formed of Dust as we are, and Dust is only a name for what happens when matter begins to understand itself. Matter loves matter. It seeks to know more about itself, and Dust is formed. The first angels condensed out of Dust, and the Authority was the first of all. He told those who came after him that he had created them, but it was a lie. One of those who came later was wiser than he was, and she found out the truth, so he banished her. We serve her still. And the Authority still reigns in the Kingdom, and Metatron is his Regent.”
Pullman uses the idea of sentient matter – he calls Dust – as a core theme of his books. This can be linked to panpsychism, which has a broad history and many proponents both ancient and recent.
But the murder of God?
The two protagonists, Lyra and Will, simply open the crystal cell that contains the Authority and he/it dissolves with “a sigh of the most profound and exhausted relief.”
There's no "fictionalized advertisement for atheism" here, however hard you look.
[0] If you are at all interested in storytelling, please read this book: https://www.goodreads.com/book/show/1602869.The_Voice_That_T...
[1] https://en.wikipedia.org/wiki/Paradise_Lost
[2] http://www.telegraph.co.uk/culture/3613962/The-Dark-Material...
[3] https://scifi.stackexchange.com/questions/118137/what-passag...