The bulk of marines treat him with the same respect they treat their Primarch, and even then thats usually far from deification.
The real problem was in the past some chapters, notably the Word Bearers, turned their faith into the core of their chapter. Once that faith was lost, they became instruments of evil.
The Word Bearers went bad because the Emperor complained about their righteous beliefs, and the Dark Angels were split because they lost faith in their Emperor and their Primarch.
On the older posts, the Warhammer world WAS considered to be part of the 40k universe. It was the Old Ones private place to experiment with life. At its polar regions were warp gates which allowed travel between it and the universe at large. These gates collapsed, allowing the leaking of chaos into the world.
There's no real clue as the location of the Warhammer world. The Slann were toast long before Slaanesh was born, so chances are the group chiefly to blame are either the C'tan (or their Necrontyr underlings) or the Enslavers (possibly other warp entities but not the "big three", they were chiefly created by Man).
Some not entirely reliable fluff states that the Warhammer world started as an experiment on the creation of a race to defeat the C'tan, and then moved on to become a race that would not succumb to Chaos. Hence why Halflings are apparently immune to the effects of Chaos (being the last creation of the Old Ones).
There is a logic to this, especially when you consider that Man created Khorne, Nurgle, and Tzeentch, while the only creatures the Eldar have conjured up have been Slaanesh and Khaine... Khaine got messed up by Slaanesh, and Slaanesh is almost a minor power compared to the Big Three. Eldar might have some impressive warp manipulation skills but they can't measure up to the damage Man can do.
