Via Will Baude: Maureen Craig is right that the transformation of the Church Authority to a secular totalitarianism guts His Dark Materials. The Amber Spyglass, which centers around the battle against the forces of the Authority, would be butchered. But could Northern Lights/The Golden Compass even retain its meaning?
As the story stands, the villains are evil but well-meaning; they genuinely think that purging children of original sin by spiritually lobotomizing them is in the children's best interests. If the religious motivation for severing is obliterated, what is left? Generic sadism? What made the story so frightening and powerful was the combination of the cool medical professionalism and religious zealotry that was wielded against the children for their own good. I am racking my brain for an equally powerful motivation that could spur the people in Pullman's world to cut themselves off from a fundamental part of their own personalities and coming up with nothing. Their desire for spiritual purity even at the highest cost explains the villains and humanizes them, while at the same time chills the reader to the core. Reducing their motive to mere cruelty undermines the story's ability to disturb and thus its power. No number of armored bear duels will make up for that.
(Updated to add a link to Crescat, which of course was my source for the link to Maureen's post.)