Board Thread:Warhammer 40k General Discussion/@comment-7232811-20130506192751/@comment-24.183.94.37-20130507171003

Well if you look at it the Emperor was trying to create a society without religion and tried to hide his children "humanity" from the imperium and chaos, he even went and berated Lorgar for trying to worship him as a "god"

but after Horus turned against him and confined him to the "Golden Throne" there was nothing he could do to stop the religious zeal anymore, so the politicians who took over and ran everything for the Emperor after he became the puppet on the throne; the politicians decided it was better for everyone to "worship" the emperor and to know that the imperium existed, of course even with the Emperor not incompacitated it would have been hard to hide "chaos" after what Horus did. but with the Emperor silenced it was easier for them to let people find out on their own what chaos is and send them tools to fight it as it springs up "inquisition"

so yes you are right, it started off as supressing religion, chaos said f that, turned horus against the emperor, politicians created the Emperor as a "god" because it seemed the best way to fight chaos without the actual help of the Emperor in the flesh.