Okay, so I'll try to avoid spoilers as much as possible, but if you are planning to run/play No Surrender, maybe skip this.

You have just finished the above campaign, and in this scenario, saved the Lycurgos. The Star Fort is still filled with benighted evil, and possibly tainted with one or more warp spirits. The book says that it will need to be "purified". Who would normally do this? Would Tech-Priests perform this task, reconsecrating their beloved machine spirits, Priests, using litanies of castigation to purge the Chaos influences, or what? I ask because I am wondering if the end of the campaign might be an interesting place to introduce Inquisitor Aldrich. As a Malleus Inquisitor, she could easily be fit to come help with the daemon engines left, might have a specially trained Magos of Banisher in her retinue, and any of a number of reasons to be interested in the slvation of the star fort, AND the team(s) who made that possible. Once things settle there, she might even "borrow" the team, and some other Guardsmen, for a mission or two of her own, as an Inquisitor can requisition Guardsmen the way Guardsmen requisition lasguns. Could this sort of fit easily enough?

It would seem to be a good "kickstart" point for the upcoming "Shield of humanity" supplement. But in any case, This would be a good game for your squad to be packing along with some specialists whose purpose would be to complete the "purification" of the station! These would definitively include Engineseers, Ministorium priests, Sanctioned Psykers and even Commissars to keep things a-movin! Certainly, As the actual Military threats started to die down the game would shift to a more DH feel as groups of specialists hunted through the station looking to repair systems and purge lingering contagions. Might even be an instance where your OW game "downshifts" into a Dark heresy campaign. This would certainly make sense with the arrival of an Inquisitor and their retinue. Such a group would be "purpose built" for the mission at hand and might include your veteran guardsmen (Your OW squad) or even a Squad of Battle sisters to serve as the "tip of the spear" in such a campaign.

For me such a purge would require all of the mentioned specialists.

You need the Techpriests to get the systems cleaned, repaired and running again.

Priests santify the place using prayers, incence and other meassures.

Sanctified psykers would be used to clean the foprtress and test the Gellar fields.

And yes, an Inquisitor would be perfectly reasonable to investigate and requisition the troops who cleaned it. If only to test the soldiers for corruption and a little purge themselves.

Exactly!

And how do players survive this scenario (the campaign)? I've whined repeatedly how Guardsmen who see Grey Knights are usually capped, since seeing such horrors as only they fight leaves "lesser" men and women damaged, if not out and out nuts. Well, no Grey Knights here, but the players will still see some hairy stuff; is there a sort of cutoff point, in game or in fluff, where the survivors DON'T get wiped, just to ensure that they aren't lost? Maybe that's what Insanity and Corrucption are for, and if the number is low still, you are deemed fit to continue to serve, or maybe "mortals" just explode, and have to be put down (that's what separates the few Inquisitors choose, and people like Space Marines, from the rest). What's a good indicator if the Commissars won't just cap you for letting Secessionists live and aide you, or Inquisitors liquify you before you REALLY fall to evil? It's always been a bit of a tough gauge for me to grasp, in a setting where whole worlds are callously cast off, and the greatest strength of Humanity is numbers of expendable chattel.

The answer depends heavily on who is doing the evaluating. Commissars tend to cleave rather precisely to rules and regulation whereas Inquisitors tend to have a somewhat broader view. Not to mention, Commissars are no more immune to mental trauma and insanity than anyone else! Inquisitors would tend to be much higher experience and thus have a greater breadth of abilities and resources to combat such things. If the Pc's encounter "Moral Threats" (Malleus Extremis) then they will of course be monitored closely for corruption. It is up to the Gm to determine the results of this. Characters who start developing unhealthy traits or mutations are in deep s*** from anything but the most radical of Inquisitors!

As to letting secessionists live to aid you? Again, who's making the call? Unless the Inquisition has declared the station inhabitants exterminatus, It will fall to agents of the Ecclesiarchy to bring the inhabitants back to the "Correct" path. IRL General George S. Patton faced significant political censure for this very thing. (He compared many German officials belonging to the Nazi party to being similar to being a democrat or republican and serving in government.) Of course Patton was not referring to the atrocities committed by members of the SS but of that didn't matter to the media who made a big issue over it! Patton just wanted to use these people to keep thing functioning because they new how! If one of your players is a senior officer than they could face the same issues. Once the "Official" battle for the station is over Politics and Intrigue will no doubt play a huge role in it's purification and repatriation. It's up to the Gm as to how much they want to get into this.

Culling is only the option taken in the most extreme circumstances. the most obvious of which being the much publicised grey knight purge of civilian survivors aftr he first war of Armagedon, but let`s not forget that wasn`t just any old fight with ol` spikey that was a deamonic incursion by Angron himself, his personal deamon legion and the world eaters.

Think about it sensibly, if they capped troopers for seeing freaky things then Cadia would be a hell of a lot quieter by now. After all you can always have a psyker just supress their memories of what they`ve seen.