There's also the theory that the Emperor had it all planned; right down to the flaws in the primarchs and the messed up way he dealt with some of them. That the Crusade collapsing and going on the Golden Throne, that being betrayed by Horus was a necessary part of creating the Imperium as its known today. For what purpose? Simply to buy humanity as much time as possible, regardless of how unpleasant that time under the Imperium might be.
Supposedly the emperor had absurd precognition powers, and was able to tell events 10k years into the future. He's also mentioned as being able to warp time in a few novels, so he may possibly have predicted all of the horus heresy, from magnus being tricked to the creation of the inquisition. This kind of makes sense actualy since, while the inquisition representes everything the Emperor DIDN'T want for humanity, its probably the only way to keep humanity from being eaten by chaos in the span of a few hundred years.
Maybe the big E actualy planned to get smashed into half life so he could stay in the warp and accumulate even more absurd powers from the faith everyone now puts in him and the millions of psykers sacrificed to him every day, all the while pretending he's actualy really frail and about to go poof, so the gods of chaos would waste time around with primarchs and individual worlds rather then just bum rushing Terra.
Maybe big E eventualy changed his mind about the whole LETS STARVE OUT CHAOS BEING ATHEISTS, since there were Xenos sucesptible to the warp and a completely faithless humanity wouldn't be enough to weaken chaos, and just decided to deal with chaos by becoming a much scarier god.
And yes, big E despised religion, mostly because of the warp. Religion is kind of a scary thing in an universe in which believing on stuff can actualy make it exist, with enough effort. It kind of makes sense in context, and its why he destroyed every church on Terra. There's even a rather famous account on big E trying to convince the last priest from the last church on Terra to abandon his religion and join him, and he almost succeeded.
Also, the eslaver plague killed what old ones were left after the war in heaven, but most of them got nommed on by the C'tan, I think, before the many C'tan got eaten by the deceiver, the void dragon, the outsider and maybe a few other more powerful C'tan. Thats the only reason the necron were able to effectively rebel against the c'tan, me thinks, since they were weakned by infighting + the krorks and eldar wraithbone thingies smacking them silly. Also the krorks may have taken part in the whole LETS EXTERMINATE THE SURVIVING OLD ONES thing, according to some sources.