If the orders appear to be coming from the Emperor, Alpharius isn't a Warmaster. Not having an official Warmaster defeats most of the point of having a Warmaster, which was that the Emperor could retire to his webway project without being bothered. If people think the Emperor's still in charge then they're going to keep trying to get in touch with him. Maybe the Alpha Legion can head of most of those attempts but remember that the Warmaster doesn't just command the Astartes but the entire military might of the Imperium, like Mars. Mars is very close to Terra, you don't think Kelbor-Hal might try to get in touch with the Emperor directly? Or what about Magnus, he can talk to the Emperor directly across space. How is the Alpa Legion going to intercept that? All in all the Alpha Legion would be so busy faking the Emperor's continued presence that they'd be quickly found out when there ability to campaign disappeared.
I was thinking of the Warmaster in the strategic sense. The one who plans the campaigns and dispatches the legions to their various objectives. Since Alpharius would be making these decisions then he would be Warmaster even if the orders appeared to be coming from the Emperor.
I agree with your point about Magnus. I've been thinking about this point since I first posted my idea and this is where my idea falls down. I think Magnus would need to be brought into the facade. My plan would be for Alpharius to buy Magnus' silence by offering him what he wants - the freedom to continue his research and modus operandi without a witchhunt against him and his Legion. Such was Magnus' vanity and certainty that what he was doing was right, I think that Alpharius offered him a deal for his silence that he'd take it. Even going so far as to accept Alpha Legion Librarians to train with the Thousand Sons. Magnus may see this as a positive sign that his knowledge and power was being accepted by the Warmaster himself. If the deal was accepted then Magnus and the Thousand Sons only had everything to gain. No more having to defend himself against Mortarion, Leman Russ and Rogal Dorn who hated the idea of Librarians and he and his Legion could operate on their own far from any prying eyes apart from the Legions who were more sympathetic to him and his Legion.
Kelbor Hal is a different matter. As we don't know exactly whether he had a direct line to the Emperor or had to use a proxy such as the Sigillite, I'm a bit stuck. If he had a direct line then he might need to be brought in. If he went via a proxy then the contact methods could be intercepted. That being said, I didn't think that the Warmaster did command the Mechanicum although I could be wrong.
For the record: the Night Haunter and the Night Lords were never official criticized, sanctioned or otherwise punished for their behaviour. At no point did the Emperor show anything but approval for their actions.
As Hailene said, Curze was sanctioned prior to the Heresy. Index Astartes II states he was called to account.
Alpharius is a smart guy (though other Primarchs are just as smart) but he's never really shown himself to be a psychological manipulator of any real skill. Many of his brothers true motives are hidden even from themselves until they are exploited in their fall. You are expecting Alpharius to know more about his brothers (who he's only know for a couple decades and even then not personally) than the Emperor knew about his sons (who he crafted for the gene up).
I'm only expecting Alpharius to know what his brothers are thinking due to extensive spy networks implanted in their Legions. The Emperor has gone to plan the Webway project so Alpharius would now need to find as much as he could about his brothers and he'd do what the Alpha Legion do best - spying.
I highly doubt that the Alpha Legion possesses the ability to infiltrate agents into all the other Legions, let alone get those agents into a position to be able to determine the psyche of their Primarchs. Remember that the infiltration of the Raven Guard took place in the complete chaos of Istvaan, an unprecedented opportunity. Other Legions have numerous language, behaviour and cultural quirks that would make them more difficult to infiltrate. And also remember that one of the Alpha Legion operatives comes very close to blowing his cover in the Raven Guard.
This point came up in another thread so I'm glad it's come up here. I agree some of the other Legions would be more difficult than others. However such is the skill of Alpha Legion that I believe that given a few years as sleepers then these operatives would be successful in hacking the Legions communication methods. Regarding the languages, behaviour and cultural quirks I think the Alpha Legion would use their Omophagea. Quietly assassinate someone who has the skills needed, eat them and hey presto. I agree this infiltration would take a while but if we're changing the whole set up then its possible the Heresy could have been prevented or at least delayed or minimised. Therefore I think the Alpha Legion would have had longer to prepare and infiltrate.
The Space Wolves, Blood Angels, Death Guard and of course the World Eaters would present their own problems but I'm thinking facial implants to disguise as the Space Wolves, face transplants for the Blood Angels, cosmetic non functioning Butchers Nails for the World Eaters for appearances sake and I'm not sure about the Death Guard due to the poisons - I'll come back to it
And of course you're assuming the Emperor would be okay with the Alpha Legion infiltrating all the other Legions (and non-Legion military bodies). And why would he be?
Since the Emperor was concentrating on his Webway, as long as the crusade continued the way he wanted and Alpharius could justify what he was doing then I don't see why he wouldn't be ok with it. Again we don't know for sure but since the Emperor was non contactable much of the time then I think he'd be happy.
This is just my theory and I'm trying to cover any holes discovered as much as I can. Hope this is ok? I'm having fun expounding on my theory