Just a warning, gonna go off on a tangent with the whole chaos invasion idea.
How long were we out?
Though the warp vision seemed only minutes, in reality the acolytes were gone for 9 years(just sounds like a good number - the number of Tzeentch). So what happened? During that time, the forces of Chaos made quick advances and great amounts of destruction, but would then cease to exist in realspace and lose ground. The Planetary Defense Forces were useless as usual, and suffered immense losses regardless.
By the time the Imperial Guard arrived, chaos sorcerers had opened numerous warp rifts along the war fronts to compensate, and ultimately the Imperial Guard had to call in for more support from throughout the sector, but still they were in a losing battle. With a chaos planetary incursion at the Imperium's hand, the importance of Barsapine became much more significant, especially due to its proximity to Scintilla. Grey Knights were called in, and your players could even be given the option to play as such.
If your players choose to play as the Grey Knights, it should be clear to the Grey Knights that they are going to need far more support, with their only chance at the moment being the Daemons' limited time in realspace, granting only short reprieves between waves before the Daemonic forces return with even greater strength and numbers. With the overwhelming odds, the nearest Space Marine chapter should be dispatched immediately, pitching this into an entire war scenario. The (lack of)success of the Grey Knights, Space Marines, and all other efforts may directly effect the survival of the Acolytes - maybe creating defensive points that the acolytes can locate, or long-lasting effects in certain areas of the planet. The war should be raging for years, and by the time the Acolytes wake up, there are far too many warp rifts on this world for even a full-scale war effort to take care of, and the planet is very nearly about to be declared lost.
With this entire sub-plot, it is playing on the epic and apocalyptic nature of the Apostasy Gambit. Barsapine should be beyond salvation no matter how much effort is invested, and the Acolytes NEED to escape, or they will die.
Escape Option A: The Acolytes might stumble on a com signal between defense forces making a last ditch effort on a beach head nearby. The Acolytes then need to somehow get from behind enemy lines into the deployment zone without getting killed by (not-so-)friendly fire. Even if the Acolytes make it to relative safety, nobody believes they are Acolytes back from the dead. Nobody comes from behind enemy lines. They will need to be properly screened once they are transported off-world.
Escape Option B: The Acolytes need to find an astropath so they might attempt to notify someone of their existence, or find out about the war effort, etc. They might travel to Hive Skaltine, where it will quickly become evident that this war-torn hive has been through years of fighting. Chaos energy and forces twist the area, and traveling into a maze-like hive city is going to be a suicidal effort. Ultimately, they will find a dangerous Astropath that has "survived" this long by fighting against the possession of a daemon inside of him.
Escape Option C: Chaos warp rifts stretch across the sky, and it is clear that there is no hope for this world. Extraction commands are being radioed to all surviving military personnel(however few there are), and the acolytes hear a broadcast from a nearby defensive location. With only minutes for the Acolytes to reach the location for extraction, they will die with the planet if they don't make it in time.
Escape Option D: Not really an escape option, but the players might decide that their acolytes are doomed to die, and simply need to send or record what knowledge they have about Arch-Cardinal Ignato. Maybe they record it with hopes that others will recover it, or maybe they seek out an astropath to send the message.
Regardless of how the Acolytes escape, they will still face more personal problems in the relative safety of the Imperium. The Acolytes have been 'gone' for almost a decade, long enough to be declared killed in action. They will have to find someone that gives a frak about their credentials, and if you're a particularly cruel GM you could make them deal with the ridiculous bureaucracy of the Administratum. Once that's cleared up, their Patron Inquisitor might have been killed in action, or might not even recognize them at first. Some more fun might be had by the GM from then on, the players facing problems whenever the Acolytes try to access anything with the credentials of 'dead people.'
The Weight of a World
If the acolytes are back in their skin(so-to-speak) and Barsapine has not yet been destroyed, their Inquisitor might ask them what they think the situation is on Barsapine. Then the decision is on them: Exterminatus?
These are just ideas, feel free to expand on them if you like any.
So anyway.. not many replies to this thread, any feedback or further suggestions?