This is the Horus Heresy, the 30K - there is no God Emperor and the ruling ideology is the Imperial Truth - rationalistic, atheistic view that Emperor tried to create to starve Chaos Gods from believers.
Simply speaking, at this stage of the Great Crusade no one heard about Chaos Gods and eventual meeting with demons was described as meeting "very dangerous xenos" (and in all fairness it was possible - the Nephilim race, while unrelated to Chaos were mental parasites feeding on their worship). Well "no one"... except the Emperor of course. He decided that "ignorance is blessing" and the "Fearless atheism" will protect his armies from falling into worship of the Ruinous Powers. He was so sure of his plan, that when Word Bearers started to worship him, he punished them harshly... which pushed their primarch Lorgar (who was always looking for something bigger than himself) to search for something else that will listen to his prayers.
As for the primarch project: Chaos gods didn't show up in person to sabotage it, but instead they created warp vortex in the secret laboratory (and, if you believe the "False Gods" novel, in the heart of this vortex was Horus himself, still not fully corrupted at this stage), so it was looking like an accident to the very few, who knew about this.
Just as a side note: even in the "present" times, not all chapters (i.e. Space Wolves) treat Emperor as god - yes, he is a great person, father to them all, worth a worship like you'd worship a great hero... but not a god.