Why is it implausible that an empire built on the interpretation of faith with religious devotion as a method of civil control would consider witten ideas a significant threat?
Yes, for significant threats. The chronicle never explains why two 'misplaced' letters are such a significant threat, which is the most frustrating thing about the story. WHY are some of the most powerful institutions in the Empire wasting vast amounts of resources tracking down misprinted books when they could be weeding out Blooder cults or stomping Minmatar terrorists? Is there something deeper about the meaning of the 'misprint', is it some kind of hidden message, subliminal mind control, or is a mark on the professional dignity of the Imperial Presses that humiliating that everyone involved in it needs to be tortured and killed, then everything in the general vicinity of that error needs to be melted? This would all make perfect sense if the book was in some way seriously heretical. But there is no indication to that. It's just a misprint.
Assuming this book is really that dangerous, the act of repression makes perfect sense for the Empire. But still, the scorched earth method still does not, because it simply would cause more harm than even potential good. I admit that practicality is not always on the mind of Imperial officials, but there is a certain point where routine destruction of settlements is going to get noticed and complained about. "Pardon me, but I was the Holder of that town and I rather liked the income I was receiving from it... Now, I understand the importance of a mandate from the Theology Council, but could you please do your operations with a bit more FUCKING PROFESSIONALISM?!" I suppose then you off the Holder and his family, silence anyone else who might have known the real truth (at this point probably a few hundred people), blame it on the Minmatar and fly off to chase the next lead. Job well done! Only had to behead the leadership and collapse the economy of a small corner of Silly Planet #143. Now to do the same to the rest!
There's a big difference between this:
"Sir, we believe the book is in this town. What are your orders?"
"Gather up suspects, interrogate them thoroughly and scour the town. The book will not escape us."
And this:
"Sir, we believe the book is in this town. What are your orders?"
"Blow it up, zero shits given."
So please, explain to me how any of this would make sense in any society besides the Imperium of Man. As I said, I really don't mind the Empire doing evil things, I just want these evil things to be complicated affairs that make sense in the end. Now, I am going to assume that there is more than meets the eye with the story described in the chron, and I will chalk it up to poor writing that it is not well hinted at. However, if you take the chron at face value it just makes the Empire seem like a caricature; an over-simplified mass of stupid government and even more stupid bureaucratic floundering. This is boring. If we're going to have something uber ebil, please take the time to have it make some sort of sense.