"There can be daemons in a secular universe."
- Warmaster Horus
"God's only excuse is that he does not exist."
"If once we can produce our perfect work—the Materialist Magician, the man, not using, but veritably worshipping, what he vaguely calls “Forces” while denying the existence of “spirits” —then the end of the war will be in sight."
-C.S. Lewis, The Screwtape Letters
"The mistake we make is to attribute to religions the errors and fanaticism of human beings."
-Tahar Ben Jelloun
"I have seldom seen a more powerful argument for the fallen nature of man, and his inability to achieve perfection, than those countries in which man sets himself up to replace God with the State."
- Peter Hitchens
The Imperial Truth is the atheist rationalist doctrine espoused by the Emperor of Mankind as part of the Great Crusade. According to the Imperial Truth, the Emperor believed that religion and superstition had divided mankind too much during its history (which the Emperor had reason to believe, having lived through most of Terra's religious wars, all of which were either fought for secular reasons or by fanatics who would have simply attached their obsession to something else if they had no religion at the time). When the Great Crusade left Terra, the Imperium of Man was to become a secular state espousing science and reason (based on the Emperor's conjectures linking religious worship to the powers of Chaos, as seen below). Following the Horus Heresy and the Emperor's internment on the Golden Throne, the Imperial Truth collapsed, the Emperor's very own philosophy denounced as HERESY wherever it was not simply forgotten, and the Imperium of Man has become a theocratic dictatorship where questioning anything results in a painful death.
However, the Emperor didn't just ban and purge religion simply because he disagreed with it. During his millennia of existence, the Emperor had come to partially determine the nature of the relationship sentient life had with the Warp. Knowing that the belief in gods would only serve to create them and empower the Warp creatures, the Emperor hoped to starve the Chaos Gods by denying them worshipers. What the Emperor failed to understand was that the Chaos Gods were powered not by faith, but by emotions. People going about their daily lives experience their normal emotions would still empower the Chaos Gods. What was needed was an alternative to direct the belief at, such as a God-Emperor (or the religions that existed at the time before Emps decided to go all Stalin on them; the Emperor may even have BEEN Stalin). Or, at least, an approach to explaining Chaos that was actually thought out. It doesn't help his case when it was later discovered during the Horus Heresy that faith actually hurts Chaos.
When Horus had a vision of the 41st millennium, part of his instant patricidal rage was that the Emperor was abandoning the Imperial Truth by seeking to become a real god (which made the Emperor a hypocrite if true). This in turn convinced him to renounce the Emperor. And then start worshiping the Chaos Gods. Chaos is a funny thing like that.
An alternative view is that the Emprah's plan wasn't to actually kill the Chaos Gods but to remove them from the Materium. The Emprah had a few major pet-peeves: religion, uncontrolled psykers, xenos and warp travel. Without Cultist-chan and chaos worshiping xenos, there would be no summoning of daemons. Without uncontrolled psykers, few possessions would occur. Without warp travel, there would be few opportunities for Chaos Gods to fuck Man up. Thus, without religion, xenos, psykers and warp travel, the Chaos Gods and their minions wouldn't be able to access the Materium (for the most part). Who gives a shit if the Chaos Gods are powerful if they are unable to do shit with that power? Answer, Emprah knows BEST!!!! (Although the Emprah withholding this knowledge from nearly everyone, including his own sons who are out on their own all over the galaxy, probably wasn't the best idea since knowing the enemy is the first step in fighting it.)
It might also be said that the Emprah didn't set himself up as a God for one simple reason: HE KNEW HE WASN'T ONE*. He is also older than those four fucks who think they are Gods. When he was born there were bad bad critters in the warp that were eating human "souls", but Ragey, Schemey and Zitpop were only just beginning to form and Rapey was still just a twinkle in the Eldar's collective eye; as such, he actually knew for a fact that there were no Gods (depending on where you sit on that in real-life) and that the Chaos Gods were delusional. Admittedly, the Emprah certainly bent the truth about the "emergent warp phenomena" often enough BUT the Imperial Truth was just that: the TRUTH.
Unfortunately, any doctrine based upon scientific materialism and skepticism doesn't work in practical terms in a universe where eternal & ethereal souls exist / people come back from the dead / technology is animistic / prayer actually works / failure to burn enough witches at the stake makes your world a putrid mess with rivers of pus / Red 'Unz do go Fasta! / and the second most advanced race in the settings is religious, works on prophecies and ghost powered mechanized support. Chaos in particular is especially irreconcilable with such things, as everything about it is contradictory and unpredictable. Not only will trying to observe it make you go insane, "replicating" it would almost certainly destroy all of reality even if it didn't work.
The Tau tried treating things scientifically on Kronus (Eldar weapons), Kaurava (Living Saints), and Medusa V (analyzing a warp rift). In the first two cases they could not understand a thing about how they worked, and on Medusa they basically made the scientific equivalent of "Here be dragons".
Magnus said that the Warp is just another type of knowledge to be used. The Warp, in turn, made him its bitch. Don't forget that at it's roots, 40k is Warhammer Fantasy IN SPACE!. Psychic powers are just the winds of magic, but they changed some details so it would sound sci-fish. Even ignoring that, there is nothing "possible, observable, and repeatable" when it comes to the Warp, and many other things in 40k. It's well, chaotic, the hate, anger and madness of uncountable beings in the Galaxy. There is nothing rational about the emotional refuse of sentience, and trying to apply scientific principles to them is a waste of time at the absolute best.
Still, the Emprah probably would have done better to be more straightforward and say: "There are no gods, just alien dimension energy beings that are so fucked up, they think they are Gods. They are lying and will fuck you over." The Emprah's own biggest fuck up was not trusting mankind or even his own Primarchs to be able to cope with the existence of eldritch entities in general without falling on our knees to worship them. Wonder how he equated that with the Cadians' daily routine of "murder the fuck out of a billion daemons" (actually, Cadia was populated by warp-worshipping primitives during the Great Crusade, but that's beside the point). The Emprah was like a manager that hides vital information from his employees because he doesn't think they can cope with the big picture. Then, the company falls apart when an engineer pisses off a major customer because of some unknown piece of said info. That is WH40K in a nutshell.
If the Imperial Truth is even known about by the time of 40k is uncertain, although more than likely the term is now used as pro-imperial propaganda by Imperial Missionaries trying to sell worship of the Emperor to disbelieving locals on your newly discovered savage world. In fact the novel Hammer & Anvil flat-out says that's what it is. Some Chaos Space Marines might remember it, but due to their worship of the Chaos Gods none of them follow it, with the exception of Fabius Bile.
* Note the word "wasn't" is strictly past tense, which is kinda important