I know 10,000 years is obviously a long time, but the Emperor decreed he was not a God and many of the Loyalists legions upheld this belief, though some obviously worshipped him slightly in secret. In 40K many of the legions now seem more religious and indeed do see him as a God. Was there a pivotal point that caused this massive mindset change?
Obviously after the Emperor was first placed on the Golden Throne, I'm sure the surviving Primarchs would have tried to continue to spread the Emperor's Imperial Truth and that surely some of this would have been passed down in their teachings to the new chapters, especially as these would have been formed from those who were aware of the Great Crusade etc. And although I know no Astartes have survived to the present 40k time, they surely would have passed on the history of their legions and the crusades and with Astartes meant to have super memories, they should remember this in their training and pass it onto each new recruit. In 40k we also have Bjorn the Fell-handed who surely would also know about this (admittedly he spends most of his time sleeping now) and speak out against it?
Was there a pivotal moment as such that changed this? Or could it in fact have been the placing of the Emperor on the Throne that caused this? i.e totally destroyed in body, yet living on meant that even the Astartes began to worship him as a God, despite what I can only assume, would have been against the will of the surviving Primarchs?