I made a few edits and wanted to make a main thread to see if I could get some input as I try to make sense of all this
With the current amount of background information made available by the introduction of the Horus Heresy series, and the often contradictory views of its many authors, there is a lack of unified theology concerning the Imperium. While this clearly reflects the divisive denominations of the Imperial Cult by the 41st Millennium, it does little for those of us who have struggled with one question more than any other in the grim darkness of the far future: “Is the Emperor a god? Or has man made him a god?” With that being said, there are three possibilities to the nature of the Emperor’s divinity.
The first idea is that, during The Great Crusade, the emperor denies the notion of his divinity under false pretenses in order to shield his people from the warp, which feeds on such non-secular sentiments. For example, if his divinity is unveiled, then how long before supernatural thinking leads to disastrous contact with the ruinous powers. Secular Humanism directly weakens the influence of the Warp, but is still a lie, though told for a righteous purpose.
The second possibility, the one that I embrace, is that the emperor is unaware of his own divinity as the physical manifestation of the Anathema Force in the Warp (God). He has yet to fully grasp his own divinity as the savior of not only the Imperium but mankind’s souls. The emperor represents not only the Messiah Archetype, or the sacrificial lamb, but specifically Author Pendragon, who will eventually return from Avalon, that place of half-death, to save his people in their time of greatest need. This time is yet to come, as humanity has so far and with tremendous struggle defeated every threat, showing its dogged determination to survive amidst unspeakable horrors. The Arthurian subtext is only fitting since so many of the Black Library’s authors are British and, try as they might, cannot steer clear of Camelot’s archetypes, which have always been the most elegant in their reflections of the human condition. What is most intriguing is that if the emperor does not recognize his divinity then he does not assume his resurrection, in keeping with the Christ figure archetype, and may thereby delay both his ascension and humanity’s salvation by prolonging his death with interment upon the Golden Throne. This state of half-death produces a god operating under limited powers. If the rules of the archetype apply within the 40k universe, then Lorgar was right when he wrote the Lectio Divinatus. I only wonder if secretly, the emperor mourned his chastisement of his son, knowing that it would lead to his embrace of chaos, but knowing that it was what was best for humanity at the time. The reason the galaxy is in such a horrible mess by the 41st millennium is due to the chief irony that provides the basis for the tragedy of the Imperium of Man and of contemporary science fiction. We have crippled the power of a god with fallen technologies. We do not have the faith needed (Perhaps not even the emperor himself) to believe that the emperor is stronger than death and so we must preserve him with the wonders of his technology and that of the Mechanicum.
There is also an allegorical school of thought which greatly simplifies the Emperor’s story-arch as a reference to Julius Caesar. This interpretation would explain the organization of the Astartes into legions, the imperial eagle icon, and , in particular, “Julius Caesar was a normal man, who conquered the known world, became a dictator, and was proclaimed a god after his death.” The miraculous manifestations, the rise of saints, and other divine incidents are, therefore, evidence of mankind being more latently psychic than previously thought and the ability of faith in emperor to banish warp spawn or protect against chaos exists merely because people believe it can, generating a rudimentary psychic field similar to the ork’s “Waaagh!” This view maintains the secular nature of 40k, but greatly inflates the depth of the tragedy to the point of grotesque satire, for all the faith in the 41st millennium loses any notion of meaning. I believe the writers do not clarify the ambiguous nature of the Emperor’s divinity so as to not alienate the secular humanist SF fans who would be loath to live in any universe where technology was not the only god. Once the mechanisms in the Golden Throne fail, the Black Library will be forced into an awkward position when the Astronomicon is snuffed out, for then humanity will either be saved by the emperor’s divinity, or the story will end and Old Night will reclaim the Imperium of Man.