My WAG, FWIW:
If you could replace the Authority / Metatron with some sort of branch of the Magisterium… The soldier of Metatron that attacks Will just before he escapes into the other world could become a soldier of the Magisterium; Mrs. Coulter could manipulate and betray the leader of the Church (a Pope figure?) instead of Metatron.
Thus the text becomes more atheist and anti-corrupt religion than anti-theist; people will still get offended, but hopefully less so.