The most offensive part to me is right here;
" As the hunt became harder, frustrations mounted and methods became more extreme, and more and more sightings were referred directly to the Ministry's elite Ordinators. Quiet infiltration operations gave way to screaming dropships disgorging armored troops into sleepy bookstores, which in turn gave way to orbital strikes against entire settlements suspected of harboring a lone copy. The Ordinators were fanatical in their pursuit and uncompromising in their methods."
Suspected. Not confirmed, or in any way sure. They obliterated entire settlements because there MIGHT be a book there, ignoring even the idea that they should double-check, or confirming that the people in the settlement was in any way in on it. Ergo, even if there was some lone person hiding in the town pretending to be a modest, innocent settler along his own faithful fellows, with a special printing-mistake in a locked chest somewhere, the Ordinators would just kill him/her along with ever single other perfectly innocent citizen just to make sure, and it wasn't even guaranteed that there was a copy there. That's not grim-dark, that down-right idiotic and moronically incompetent.
"Sup guys, I hear there may be, possibly be this guy, in Dam Torsod, hiding out with a few of these books. Maybe. Bring ya fleets and let's go glass the capital, just to be safe, yeah?"
Another annoying factor is that not even the 40k Imperium is this idiotic - the Imperium, on occasional, burn entire planets down. But this nearly always has a good reason behind it - full-fledged heretical chaos incursion that will be/has so far proven to be far to costly to remove, massive alien invasions that will be completely to costly to remove. Human lives is the imperium's greatest currency and they count in it. If it costs millions of Guardsmen to clear out a planet and this is worth taking the planet back, in the poor bastards go. If not? Viral-bombs from orbit.
This even goes all the way down to the same small-settlement scale - they get torched every now and then, but again, for reasons usually understandable. Treason, heresy, collaboration with aliens, incompetence, etc. As far as I can remember I've yet to read a 40k story involving the Imperium flattening some settlement because there might be one heretic there, or whatever. Usually they send in some troops for that, or in the case of heretics, the Sisters/Inquisition makes a visit. Or even the local planetary guard forces and their attached imperial priests, even. Nukes from orbit is usually not the first and only option considered, let alone used...