Phillip Pullman's "His Dark Materials" trilogy, the first installment of which is the basis for the poorly done (but visually beautiful) film adaptation entitled "The Golden Compass" (the first installment was released originally in the U.K. under the title "Northern Lights"), has made headlines for the premise of the plot: Killing God.
From the perspective of someone like myself, an atheist who has read all of the books (and seen the movie), Pullman's trilogy hardly comes across as an atheistic screed, and his brazen interview comments come across as little more than hyperbole designed to fuel controversy and secure book sales.
If you troll atheist discussion forums for any length of time you will no doubt encounter the aphorism that God doesn't exist and if he did the person speaking would join the side of Satan against God. One of the lesser known arguments for atheism is the moral argument against God that states that God's conduct in scriptures is so immoral that surely no such being can be a true God worthy of worship and devotion. Pullman's trilogy is essentially an elaboration of that aphorism.
The theology of the books, while not in accord with Western Christian orthodoxy theology, is closely wed to that ideology and is not atheistic. This is a trilogy in the image of "Paradise Lost." Pullman's gods and souls are more real than many religious people in real life believe deep down. His religion is probably more orthodox than his science.
Instead of a trinity, his series offers, at least, four gods, and that is without counting either Satan (or his successor in a second war with rebel angels), or Jesus. The original Satan is just an offhanded reference -- the current rebel against Heaven is not an angel but a human. Jesus is no where referenced or mentioned.
Logically, the first god is the "Creator", who by my favorite definition (a powerful non-human being acting with moral purpose in the universe) may not even qualify as a God because the Creator, like Newton's clockwork god, seems disengaged entirely from the universe.
Two more gods emerge in this theology 33,000 years before the present. One is the "Authority" who is a stand in for the Old Testament God the Father figure. He is described as the first created being, who lies to claim that he was the Creator to those who follow him. The other is "Dust" which is an omniscient, omnipresent karma-like, fate-like, Star Wars "Force"-like, trinitarian Holy Spirit-like phenomena of conscious subatomic particles that act with moral purpose in the universe and is intimately connected with sentient life force and people's souls. Dust may or may not have some identification with the Creator. The Neolithic revolution is roughly tied to an evolutionary development that allowed people to interface with Dust.
Finally, the fourth god, Metatron, a powerful angel who is a regent for the Authority who has lost his mental faculties and is aging a hair's breadth from death. Metatron, who has ruled for the last three hundred years, is connected with the particularly nasty, witch burning side of the church. Around the same time, people in an alternate universe devise a technology that starts to unravel the structure of the quantum mechanical many worlds, ravages their own world, and it appears that the leakage of Dust into the Abyss between those worlds as a result may be what has tipped the balance of moral forces in the world in the wrong direction, and may even be what has allowed Metatron to grow in power.
In Pullman's theology, every person has a living body, an intellectual self, and a soul (visible in some worlds as a Daemon who takes the shape of an animal familiar that represents a person's personality). Heaven and Hell are lies -- the land of the dead is instead a purgatory ruled by cruel Harpies. Most worlds with sentient beings have some cruel church, and in the world of Lyra, our protagonist, Calvin in Geneva was the last Pope and he abolished the office effective upon his death in lieu of a bureaucracy that secured the reigns of temporal power in much of the world and has been corrupted in the process.
The death of the gods
The Creator is never encountered, challenged, questioned or killed.
The Authority dies in the Amber Spyglass, amidst a war between the forces of Heaven and those rebelling against it, but quietly, as much of old age as anything, when Lyra and her companion innocently and with the best intentions free him from a crystal chamber that provided his frail being with what amounted to life support. God's death is more like the implementation of a living will than it is a homicide.
Many of the focal figures in the rebellion against God are hardly models of virtue. Lyra is a pre-teen, wild, selfish pathological liar who is nevertheless loyal to her friends and not actively malicious towards others. Her father, Lord Asriel, is a disgraced, ambitious Machiavellian aristocrat who leads the rebellion against god and has largely abdicated his parental duties to one of Oxford's colleges. Lyra's mother, Mrs. Coulter, is a psychopathic mad scientist and high church official who steals children from their parents so she can do unethical experiments on them to learn about Dust, who was denied an opportunity to raise her daughter, and who(contrary to the movie) does not reveal her parentage to her daughter until she is already aware of it.
Lord Asriel and his past lover Mrs. Coulter, acting together, vanquish Metatron, through a combination of a massive battle between Heaven and those rebelling against it, deception, and brute force applied to the point of self-sacrifice.
Lyra and her male companion (a boy named Will from our world, with a more pure heart) restore the structure of the many worlded universe, empty purgatory for the price of a loss of connection to their own souls, and restore Dust to its rightful place in the universe.
In short then, rather than killing god, our protagonists merely depose an illegitimate usurper and restore a true god, something of a trinitarian Holy Spirit, to its rightful place. A greater universal spirituality overcomes baser physical deities.
This isn't to say that the church of Lyra's world isn't condemned for its intellectual rigidity, its hypocrisy, its cruelty, its unearned righteousness, and its contempt for human pleasure and happiness. The Magisterium of Lyra's world shares all of those features, and it is implied that churches in other worlds are similar, and that some of this is Metatron and the Authority's doing. On the other hand, in Lyra's world, the Magisterium is the patron of science where that discipline is called "Experimental Theology" rather than a direct adversary of science.
But, the Magisterium is not monolithic. It is fraught with infighting. The only god who is killed in a homicidal fashion is killed by one of its own. The Magisterium is portrayed as almost, but not quite yet, having returned to the barbarity of the Spanish Inquisition. Its intellectual rigidity, while more vigorously enforced, is almost more a parody of the quasi-religious ideological battles that play out within the modern scientific establishment than those seen in the real world church. Its cruelty can be attributed in significant part to the rise cruel human beings to positions of power in parts of its Pope-less bureaucracy whose powers are amplified by their willingness to be ruthless. Rather than being strictly anti-Catholic, Pullman's series almost implies that having a single individual as a Pope at the helm helped the church retain a humanity that it lost when the papacy was abolished.
The Magisterium does suppress free inquiry, but comes across looking rather tame compared to many contemporary Islamic regimes or the kind of Dominionist visions of good government expressed by people like Republican Presidential candidate Governor Huckabee.
Unlike the Anglican Church that more than any other is a model for the Magisterium, it does not see its theology watered down as a consequence of becoming an established church.
Is Pullman A Threat To The Church?
The real theat to the modern Christian church in Europe is not rebellion, but apathy, or as our current Pope has described the phenomena, secularism. Pullman's His Dark Materials trilogy is not a secularist screed. His world is one in which god's reality is undeniable, and god's power is real. If anything, the controversy over these books may help the church by creating a perception of threat and giving people a strawman to fight against.
The tradition of men arguing with god over perceived injustice is ancient and scripturally orthodox. Pullman's trilogy is more in the tradition of the biblical story of Jacob, at its climax even featuring humans wrestling with an angel, than it is an argument for atheism.
Perhaps the biggest threat to the church of all from the trilogy is Pullman's audacity. Surely, anyone who can write novels about killing god must be comfortable that there are no gods who would take offense at them. Pullman adopts the modern truism that morality is in the eye of the beholder. Pullman reduces Christian theology to the level of fairy tale and then twists it, much like Gregory Maguire does to the Wizard of Oz series in Wicked. Pullman's books are almost incomprehensible from a sincerely Christian worldview, and if you read it and get it, you may have sown the seeds of doubt by acknowledging that your root assumptions about the world aren't the only ones possible.
But, few people in the modern world who read well enough to finish the books are innocent enough not to have had those assumptions challenged already. The scripture themselves already contain more than enough seeds of doubt when juxtaposed against the modern world, to put the church at risk of irrelevance.