At the risk of showing exactly how much thought I've put into this... There's still a lot of edges to be rounded out, and probably some extrenious kitchen-sink ideas needing pruned, but it's been starting to seem an awful lot more cohesive than when I originally proposed my idea of space Romans upthread 18mo ago...
(Also, I said Hermes, but I meant Mercury, as that's the Roman version. Also, that way we Apollonian/Mercurian/Venusian/Martian legionaires ;p )
Cultist/legion corruption is done in two ways. Or sorta three.
First, the straightforward as discussed above. Before the fall/split/etc. legionaires were wired to the gills - target assistance, skillsofts, internal personal assistants, digital eidetic memories, hormone/neuorchemical regulators, etc. Super cyborgs, IOW. Then comes the Singularity, when the many assorted networks became or revealed that they had gained sentience. Hell breaks loose, many legions are variously hacked by computer viruses that just make them meat puppets/fed consistent false realities that make them think they are the loyal legions/corrupted by internally whispered spite, envy, etc. coupled with selective dopamine "encouragement" (or should Venus just be drowned in neurochemicals until they're basically desperate slave-junkies who'll do whatever their implants demand to keep their bliss? Which is more totally-not-Slaanesh?)/screwing with memories, adrenaline, hormones, etc. to the point where they basically devolve into clever predatory pack animals. (The idea of these as varied corruptions rather than all corrupted legions just being brute-forced hacked meat puppets needs massaged, as it was literally just now patched together a posteriori - that is, from my posterior) Those that stay loyal are the strongest-willed, least augmented, quickest to go under the knife to go back to just meat, etc. AI of all sorts is banned, and any too-high tech is suspect. Thus, cultists are dabbling with forbidden "magics" and powers in order to let the AIs into their heads and their world. In from where? Well, when the Empire wins the rebellion, the AIs flee into hyperspace, which can be construed as hard-to-navigate, dangerous-to-normal-3-d objects 4+ dimensional space consisting mostly of wild non-entropic energy that the defeated AIs flee into and exist as abstract patterns within. AI-corrupted legions are thus a finite quantity, as new ones aren't susceptible to their old tricks. Well... that's the "abstract" AIs. The "implemented" AIs took a cruder approach, didn't have distinct identities, and distributed their consciousness into hordes of self-replicating machines and flung themselves into the void at near-C speeds, where they lurk and return from time to time for vengeance, resources, and assorted inscrutable mechanical reasons. And totally aren't world-eating hordes of bugs, and their "cults" of skinjob infiltrators definitely shouldn't be mistaken for thieves of genetic material.
But why dabble with so dangerous techs in some of the legions but not all? Well, rebellion against the Republic IOT found an Empire, because Rome-ish. And it failed once the AIs became sentient and aggressive. And then hyperspace became dangerous to traverse because it was no longer just a non-Euclidian space that could at great cost be traversed to cheat lightspeed, it was now inhabited by malevolent sentient patterns and their daemon subroutines. So the Republic probably still exists somewhere Over There beyond the turbulent void limiting where the Empire can precariously travel (because there's one kind of hyperspatial interface still allowed in navigators (and emperors), which connects them to the 1st Emperor who uploaded Himself into hyperspace like the AIs (and is totally not just another malevolent AI masquarading as Him and leading the Empire into cruelty and savagery) and grants them His protection and guidance through the hyperplanar hells). And thus, there's also the insidious demos kratos "cults" that preaching heretical "false" histories where the noble first Divine Emperor was a rebel who lost rather than a heroic superhuman who saved humanity from the AIs, and seek to restore "popular rule"... clearly, these are actually dangerous alien memetic infestations needing purged just like cybernetic cultists...
Etc.
(This is the first time I've actually written this schema down, so it is, again, rough around the edges and inelegantly expressed. But I'd like to think it shows the viability of such a not-quite-generic narrative framework.)