[@Letter Bee]
Chaos was born from the War in Heaven. The Chaos Gods draw strength from fear, destruction, pain, suffering, and disparity. However, in addition to this, they draw immense power from Faith. It was stated that during 'modern times' the Chaos Gods were drawing power from all religions, the faith of humans allowing them to tap into all human emotions. To an extent the faith of humans formed the consciousness of the Chaos Gods, who emerged from the mere Chaos that had existed before around the Dark Ages. Even the peaceful and friendly religions were feeding their power, and the Emperor, realizing this, sought to spread atheism. But it was only after the Apocalypse that he made his presence actively known, forming the Thunder Warriors and actively guiding humanity on it's path to prosperity. 

Keeping people informed about Chaos is a double-edged blade. Psykers are like a beacon to Daemon, but those unaware of the existence of Daemon are warded by their ignorance, to an extent. Psykers who are aware of Chaos gain the ability to perceive it, however, and in turn can be more easily affected by it. Furthermore, it vastly increases the risk that someone would call out to the Chaos Gods. While to an objective observer they are clearly beings of pure evil, to someone with limited knowledge they might seem close to benign, and the Chaos Gods have often granted gifts or boons to mortals in exchange for worship. Except Nurgle, because he considers diseases gifts, so nobody likes him.

Also, the Emperor wanted to leave Interex alone. It was Horus who ordered the destruction of Interex, and used this event as a tool to assist in turning Magnus towards Chaos.

As a devoted 40K fan, I trump your mere wiki knowledge with obsessive research and owning many of the books.