He is following in the footsteps of the great eighteenth-century Enlightenment critics of religion like Voltaire who sought to undermine the authoritarian power structures of their day by challenging their religious underpinnings. So long as the Church endorsed slavery, the divine right of kings, and censorship, the sort of liberating changes the rationalists yearned for could not come to pass, unless the Church's authority could be called into question. Similarly, Rushdie sees modern societies like Iran and Pakistan as cursed by religious convictions that bring out the worst qualities in their believers. The entire novel strives to break down absolutes, to blur easy dichotomies, to question traditional assumptions of all kinds. Demons can behave like angels and vice versa.
High ideals can lead people to commit terrible crimes.
Love can be mixed with jealous hate. Exalted faith can lead to tragedy. Just as Rushdie strives to destroy the distinction between center and periphery, so he challenges easy distinctions between good and evil. At the end of the novel, Saladin returns to India, finally to reconcile himself with his father. But this is no simple return to his roots.