I mean broadly speaking, GSC shouldn't exist now the new malstrain rules exists as, fluffwise, those Genestealer Cults that still exist on Necromunda are the faded vestiges of the original Secundus event...
Not completely correct.
GSC spread out from Secundus before the Dust Wall was finished, then Hive Secundus was bombarded with rads and grav bombs.
Those GSC were not bombarded with rads and grav bombs etc, and could be considererd "original recipe" Malstrain Genestealers.
The Book of Desolation makes it clear on page 47:
Interestingly, where Malstrain cults emerge in hives and outland settlements they are often in opposition to the more stable strains of the Genestealer plague. From time to time Genestealer spore will be brought to Necromunda on one of the billions upon billions of cargo containers endlessly passing through the Eye of Selene. Sometimes these make their way down into the underhive where they can take root. As the fledgling cult grows it detects the corrupted psychic signal of the Malstrain Patriarch, projected from the ruins of Secundus. As often as not this signal repels the cult, though some do succumb to its call and make their way to the Abyss to be absorbed into the Malstrain cult.
The "as often as not" or 50% of the time vanilla Genestealer Cultists (either present prior to the Secundus outbreak or imported) don't succumb to the Malstrain Patriarch's psychic signal indicates that there are still active Original Recipe Genestealer Cults on the surface.
Similarly, Chaos cultist and GSC should be mutually exclusive, since by nature a Genestealer Cult is dominated by the influence of the Patriarch and by extension the Hive Mind, doesn't leave room for independent worship of the Chaos Gods.
The
Cult Tenebrous example that always comes up in debates about this is interesting, but its extremity demonstrates why it shouldn't be possible on Necromunda.
For those who don't follow the link, that Genestealer Cult's space vessel was "
swallowed by a Warp Storm that stranded them on the outskirts of the Garden of Nurgle in the Realm of Chaos".
There's a significant difference between being a GSC patriarch mind-controlled cult corrupted by exposure to Chaotic energies within the deepest parts of the Immaterium, and the same sort of cultists being exposed to the low-key chaotic stuff that could be found on Necromunda - remember, Helot cultists don't even rate Lesser Daemons on their roster!
Saints Crusade you could play either way, I actually think the idea of a Saints Crusade actually being a Chaos or Genestealer Cult being entirely in keeping with the setting, for example.
The Saints Crusades rules have sufficient downsides if you fail to meet the Saint's demands that it's probably better permitted under the rule of cool than not.
But they're probably drawing on the same power source as that which provides Cawdor their crunchy free faith dice and which explicitly forbids Chaos or Genestealer taint.
Compare Faith Dice [page 97, Book of Faith]:
These dice are a resource that all Cawdor gangs (except those that have become Chaos Corrupted or Genestealer Infected) generate over the course of the battle.
With Pledging to a Saint, [page 51, Vaults of Temenos]:
During any campaign, any gang, whether Law-abidingor Outlaw, can pledge their service to a Saint so long as there is not already a call upon them. This means that Corpse Grinder Cults, Genestealer Cults, Helot Chaos Cults, Chaos Corrupted gangs or Genestealer Infected gangs cannot pledge to a Saint.
Secundus/Desolation wasn't out at that point, but is anyone really claiming that Malstrain cultists don't have a psychic link to the Malstrain Patriarch that is intended to be considered to be a calling on the same order as Chaos Taint or the OR GSC?