[Tema69]

Ex-Adept Mechanicus might work as the ones with tech-knowledge. I guess surviving members of the Mech Cult might have integrated with the emerging civilization (post-civil-war), and have become somewhat different during the generations.
But they (and perhaps the top echelons of the government), might be the only ones with any real access to military grade high tech gear (and decryption devices for the data facilities). Thus, snatching one might prove dangerous.

I really like the whole nurgle-worshipping-agent-helping-the-pcs-secretly idea, but to minimize (my) confusion, perhaps we should slap that idea on top of the what's-that-ship-that-just-boarded idea. How about said Nurgle worshipper(s) boarding after the PCs to create a psychic beacon for the now-corrupted troopships to home in on, while for the first time taking active part in the whole thing, by preventing the PCs from blowing up the Star Fort.

Also, to give the PCs a hint of Nurgle influence, they might discover whole areas killed off by Nurgle Plagues (Chaos agents helping the PCs with eliminating local lifeforms) while the PCs are rounding up civies in extermination camps (keep in mind the inspiration for the Inquisition is stuff like the Gestapo and the KGB) and virus bombing forrests etc, to deny the nids any advantage they might gain from attacking the planet. That might not make any sense to them at first, but they might connect the dots later on (if not, I'll be sure to insert some sort of debrief, one way or the other).