Theocracy ended with the acceptance that most people will end up eternally damned as there can't be two competing religions holding the complete truth and Europ

Theocracy ended with the acceptance that most people will end up eternally damned as there can't be two competing religions holding the complete truth and European population was quickly fractured into "us vs heretics" depending on the side one was on, whereas before everybody was part of the same church. That weakened religion and allowed rationalist thought to emerge.