Sorry for the thread necro, but since the previous conversation never reached a conclusion, I thought to offer my two cents.
Regarding canon: According to Dan Abnett, Gav Thorpe, our own ADB, and others, Warhammer 40K doesn't have anything resembling hard canon. There are some broad common elements, sure, but each author is free to cherry-pick elements they like and discard those they don't. That's how we can end up with backflipping terminators with multilazorz and Slaanesh-worshiping pedophile Farseers, although since then BL has tried to keep such egregious flights of fancy to a minimum. The Horus Heresy series in particular is supposed to emphasize consistency and continuity, as it is a team effort in many ways.
Regarding the Emperor's origins: Whether you prefer studio material over Black Library or vice versa, at no point has the original shaman story been retconned or explicitly stated to be invalid, and no alternative storylines have been proposed. Therefore, in as far as there is canon in 40K, the shaman storyline remains "official".
The same can be said about the Illuminati (although I don't like to think about those books; despite the torturous writing style, the first two managed to set up an interesting story, but the third book wasted all that potential on stupid irrelevant bullshit).
Regarding Lorgar in The First Heretic: The perception of Lorgar as weak is not just the whining of a few fans, but a sentiment I often see expressed in various forum discussions. He comes across as a religious nutjob desperate for something, anything, greater than himself to believe in and give his life meaning. After his ludicrously over-the-top chastising by the Emperor, he lets himself be manipulated by a corrupt old man and a power-hungry Astartes. Kor Phaeron and Erebus seem to mastermind the whole Heresy, while Lorgar is off seeking his answers. And even when they arrive at the Eye, he sends his Captain to get those answers in his stead. This sentiment extends to the characters in the book, as well, with most of the Primarchs except Magnus seemingly holding Lorgar in contempt, and I'm pretty sure at one point the Custodes assigned to babysit him refer to Lorgar as "this weakling Primarch". If in the new novel Lorgar has finally decided to "nut up", then ipso facto he was not "nutting up" before, i.e. being somewhat of a pansy.
Speaking of the new novel, I have yet to read it, since the only way to acquire it right now is to shell out $80+ on eBay. BL seems to be determined to keep people from reading this book. Anyway, I'm glad Lorgar has toughened up, but I have to raise an eyebrow at some of the feats described in this thread, as they are approaching Wardian proportions. I can buy it if at this point Lorgar has fully committed to the Chaos Gods and is well on his way to Daemon Princehood, but if such prowess is merely the result of him "nutting up", then it feels very much as gratuitous over-compensation. I mean, out-psykering Magnus? Really?