In my game, I give out xp through a system of questions. The first 10 or so are questions about the mission they are on, which I score secretly depending on how close they are. The second half are team questions based off what the party did, and they have to convince me that they achieved these. For example some would be:

Did you eliminate a threat to the imperium
Did you make a new ally
Did you sacrifice anything irreplaceable for the imperium

If they did these things and can convince me of it, I give them xp, usually between 20-30 xp.

The question that I am having difficulty marking is this: "Did you Improve the lives of the citizens of the imperium in the area you where in."

The answer that has been given is this: "Yes! Through our actions, the faithless dogs of the Hive of the Emperor’s Light, have been shown the error of their ways! Clearly, Cole’s psychic phenomena was no coincidence, and was meant as a sign of the almighty God Emperor’s displeasure with the lack of faith in the populace. Through his almighty will, using Cole as the messenger of his disappointment in his people, the people have paid the price for their sacrilege, and those that remain after the purge will remember the bloody rains that their heresy summoned. Having seen the price of their sacrilege they shall be more mindful of the Emperor’s holy designs and of his servants, and their piety shall improve as a direct result. And what life could be better spent than in service to the Emperor?"

For reference on what happened, the parties psyker rolled a 9 on a test and summoned bloody rain, several events later this led to the ecclesiarchy purging the whole hive block, killing countless thousands. However it had been noted that prior to this there had been resentment by some of the citizens and general dislike of the church in the area. When the fighting purging broke out, some of the citizens fought back, which made the whole thing much worse.

I am conflicted if I should give this to them, as on the one hand, they killed probably thousands of innocents because of their mistake, and have only helped reinforce tyranny. On the other hand though, its 40k, and those peasants did not worship the holy god emperor of mankind, who rules from holy terra with grace and supreme authority nearly as much as they should have!

(Should be noted none of the characters are overly all that much of a zealot)

I believe yes, you should. The player clearly took creativity from an in-verse point of view to demonstrate how they improved the lives of the imperial citizens. Those that had been purged were clearly no longer imperial citizens when they decided to fight back against their teachings, and those that replace them will do will to remember what happens to those who lose favor with the God-Emperor.

So my vote is yes - excellent in character rationalizing.

Since they're not fanatics of the Emperor, I would maybe give them 1-3 insanity points and give them their XP.

Inocents?! There is no innocence only degrees of guilt! The loyal citizens should not have stood ideally by as their neighbors became traitors and heretics! A purge of the area with the righteous flame of the eclesiarchy was the only true solution!!!

Out of Character, I'd give them the XP and 1 insanity. I'd also warn them that there may be more insanity point do come if they don't RP being such zellots, as there characters realize what they have done and their excuse begins to grow thin in their own minds.

Ah the age old problem of DH - the purging of countless lives being a "normal" thing to do. I'd say give them xp, but also a few corruption and insanity points. Killing should never be taken lightly, even in 40K and it should weigh heavily on their souls.

The value of human life in 40k is extremely low. It is, in fact, the one resource the Imperium never lacks for. A few thousand getting killed in an Ecclesiarchal purge is probably less than the total number killed in the weekly queue-riots outside the local Administratum office. As noted, as well, those killed were found wanting in their faith, so if the Acolytes had not been the catalyst for the purge, something else most certainly would have been. There's a number of quotes in the setting that illustrate just how zealous the Imperium can be, and just how dystopian the entire setting is. "Many are called, most are found wanting" "To fear the Inquisition is redundant; to hate them, heretical". There is, also, the justification that the player gave. Their character is, obviously, sufficiently zealous and, as the saying goes, "zeal is its own excuse".

Reinforcing tyranny is the name of the game for the Inquisition. "To begin reform is to begin revolution". Some Inquisitors do try to swing things the other way in the Imperium... they are, of course, rightly condemned as Radicals. This game is a dystopian setting of the darkest shades of grey, and just about anyone who seems to be a paragon of virtue and heroics is probably a pawn of the Ruinous Powers, fully steeped in the ways of the Warp and speaking with the tongues of daemons. It is a setting where the most terrible thing is happening to everyone, everywhere, at the same time and every horrific decision, every death, every man, woman and child living in the worst conditions imaginable is the result of the absolute best that can be done. Every day requires one to sacrifice a little bit more of their humanity in order to survive and all it asks is if it would, perhaps, have been better to die.

The value of human life in 40k is extremely low. It is, in fact, the one resource the Imperium never lacks for. A few thousand getting killed in an Ecclesiarchal purge is probably less than the total number killed in the weekly queue-riots outside the local Administratum office. As noted, as well, those killed were found wanting in their faith, so if the Acolytes had not been the catalyst for the purge, something else most certainly would have been. There's a number of quotes in the setting that illustrate just how zealous the Imperium can be, and just how dystopian the entire setting is. "Many are called, most are found wanting" "To fear the Inquisition is redundant; to hate them, heretical". There is, also, the justification that the player gave. Their character is, obviously, sufficiently zealous and, as the saying goes, "zeal is its own excuse".

Reinforcing tyranny is the name of the game for the Inquisition. "To begin reform is to begin revolution". Some Inquisitors do try to swing things the other way in the Imperium... they are, of course, rightly condemned as Radicals. This game is a dystopian setting of the darkest shades of grey, and just about anyone who seems to be a paragon of virtue and heroics is probably a pawn of the Ruinous Powers, fully steeped in the ways of the Warp and speaking with the tongues of daemons. It is a setting where the most terrible thing is happening to everyone, everywhere, at the same time and every horrific decision, every death, every man, woman and child living in the worst conditions imaginable is the result of the absolute best that can be done. Every day requires one to sacrifice a little bit more of their humanity in order to survive and all it asks is if it would, perhaps, have been better to die.

One of the best summaries of Warhammer 40,000 that I've ever read. Well done, good Sir.