Horus Rising was published in 2006, and in it, Garviel Loken is staunchly adherent to the "Imperial Truth", as described in his induction to the Mournival:

Loken nodded again. His feeling of being unnerved had returned, sharp and unwelcome. This was a ritual, and it smacked dangerously of the practices of corpse-whisperers and spiritualists. The entire process seemed shot through with superstition and arcane worship, the sort of spiritual unreason Sindermann had taught him to rail against.

He felt he had to say something before it was too late. 'I am a man of faith,' he said softly, 'and that faith is the truth of the Imperium. I will not bow to any fane or acknowledge any spirit. I own only the empirical clarity of Imperial Truth.'

Since the Horus Heresy has continued with this, it's easy to forget how novel that was. Just four years earlier, the original Index Astartes - Word Bearers, in White Dwarf, is very clear that the Imperial Cult was already in place during the Crusade, and that Lorgar was an apostate and heretic from it; his sin was not faith, but excessive faith, before his fall to Chaos. That IA article begins thusly:

Lorgar, Primarch of the Word Bearers Legion of Space Marines, was known as one of the most scrupulous and dedicated followers of the Imperial Cult. His zeal in persecuting the enemies of the Emperor was almost unmatched by any of his brother Primarchs and many were those who felt him to be the most devoted of the Primarchs.

Also, at that point, Erebus didn't exist. All his considerable dickery was instead the product of Kor Phaeron, in addition to Phaeron's own, leading to now-unprecedented levels of concentrated asshole. Though he did avoid the "terrible father" parts; in the IA's telling, he was an ambitious peer of Lorgar, who egged him into sharing his prophetic vision of the golden man with his congregation and the faith at large, not an old man who raised Lorgar viciously.

Note also the distinct lack of Chaos worship in this description of Colchis and the Covenant, and in the reason for their civil war. (Also Magnus was still a Cyclops from birth at this point. On that front I entirely agree with the switch.)

In his description of Colchis, Carpinus tells of a caste of priests calling themselves the Covenant who rebuilt the shattered society of Colchis on the promise that a great leader would one day come to deliver them from the darkness their world had descended into. With harsh religious observance, the Covenant's strict dogma became a gigantic, monolithic belief structure that permeated every facet of daily life on Colchis.

...

The Speculum Historiale speaks of a tale told by Lorgar to Konrad Curze, [...] Lorgar spoke of strange dreams and visions that afflicted him in his early years. In them he saw a mighty warrior in gleaming armour with a helm of bronze and a shining sword. A giant in blue robes with but a single, unblinking eye stood behind him, speaking of his lord's coming to Colchis and that Lorgar must be ready for him. Lorgar was convinced that this mighty warrior was the divine leader the Canticles of the Covenant had promised and, at the urging of Kor Phaeron, his closest friend, began spreading the word that their god would soon be amongst them. People flocked to hear his words and waves of popular support followed Lorgar wherever he preached. This was the opportunity Lorgar's enemies within the Covenant had been waiting for and they denounced him as a heretic, fearing the threat to the status quo and their power.

This also extended to the Word Bearers; they weren't the first worshippers of the God-Emperor, they were merely far more devout and fanatic than any others.

Jarulek himself captured the planets ruler, throwing him to the blood-maddened survivors of the battle at the gates. Fully 90% of the [fanatic converts] who had joined Jarulek s march were dead, while barely a handful of Word Bearers had been killed. Following the victory, Jarulek began indoctrinal teachings among the populace and when Adepts of the Ministorum arrived to bring the word of the Emperor to Fortrea Quintus, they were horrified by the Word Bearers careless use of the populace, but found the people as well versed in the faith of the Imperium as any loyal world could be.

Historical note: Fortrea Quintus was later cleansed by the Blood Angels after the planet sided with Horus during the Heresy and the citizenry rose up to slaughter their Imperial leaders. It is widely believed that the Word Bearers corrupted the populace on the planet's initial capture.

When noting the weird contradictions in the worldbuilding of 30k, it's good to remember that they mostly exist because the beginning of the Horus Heresy novels made fairly massive changes to the existing background.