He IS missing his hand as his gauntlet was the only thing recovered during the fight against the Despoiler along with the skeletal remains left within. Implying that he went missing since the first Black Crusade, and depending on the time frame of this roleplay, that's a good millennia to be marinating in the warp and its corruptive influences and as proven by lore, Primarchs are far from incorruptible. Leman Russ and Corax are both AWOL and are one of the very few cannon loop holes of unconfirmed history. Corax however was confirmed on a collision course to the Eye of Terror so he probably died or was corrupted.
Maybe you're right but keep in mind that none of the lore is ironclad. the fate of the primarchs probably so but the other stuff may be able to stay "relatively" pure under the proper circumstances. You know more about the lore than I do and I'll be the first to admit my own ignorance but I do know the lore here doesn't work the same way lore works in Star Wars or Star Trek. we don't have absolute truths to work with and there's a lot of gray area and half-truths. I'm saying this because I have a few ideas that may go "against" the canon. the goal is to be creative, not to be sacriligious or to "ruin the lore" so to say. try to keep that in mind as we proceed.
I will say this however: There are no primarchs here. I don't know their history nearly well enough to somehow write one back into existance. but even if I did, so what? This is supposed to be fun. An opportunity to explore the "what-ifs" of this universe. a humble forum on the internet is exactly the place to do this. Certainly better than a Black Library book with "official" canon!
Lore for Warhammer 40k goes as follows: Official Codices, Technical Documents, Games Workshop Official Q&As, Games Workshop Novels and Short Storys (It has to be stamped with GW on it or it doesn't count) Artistic License Holders such as development studios, commissioned writers, and their affiliated support staff. Anything they write that is not already dictated by GW is considered canon but if they write something GW has already made a ruling on, GW overrides regardless. Anything written by a commissioned writer AFTER their license has expired or been revoked is no longer considered canon. Third party license supplements such as the Space Hulk boardgame or the Rouge Trader RPG These are considered separate from Artistic License Holders because their terms of use are to a very specific segment of the Warhammer Universe and that only. These are barely considered canon in most cases. Fan-Lore. Is never considered canon and can be hit with a 50/50 you can choose to believe it or not until an official ruling is released.
The same way it works for Star Wars, you take official sources over everything else first. It's a terrible system because it implies tabletop stats are a direct representation of the unit it represents but that's how everything is handled. They're the owners so they get first and final say over everything.
That's been one of the more frustrating parts of the lore for me and partly why I've done as much reading as I have before trying something like this. If space marines really were represented as they were on the tabletop they'd need chapters of thousands to be effective. Dawn of War made that perception even worse. You can imagine how surprised I was when I actually started reading their background :O
For the record, I'm very much enjoying your twist, and look forward to seeing how it plays out into the plot.