The Great Crusade was all about abolishing superstition and religion from all Humanity in the galaxy and leading the Imperium into an era of enlightenment and understanding.
So then why do Astartes from the HH series, which takes place towards the end of the Crusade, refer to things as Heresy? Heresy is an act/statement that is contrary to religious belief isnt it? So why do the champions of the Emperor's cause link themselves to a concept they are sworn to destroy?