What is a synonym of "destroy," when the thing destroyed is a collection of documents. The destruction is intentional because the documents are not considered to have come from the authorized source of learning. In essence, the destruction is really to disable dissemination. Thanks.
I'd suggest expunge.
to eliminate completely; wipe out; efface; destroy (Random House)
to erase or remove completely (something unwanted or unpleasant)(Oxford)
Church has expunged books and passages that failed to toe the doctrinal line.
Another mistake we humans have made through the ages, and occasionally continue to make to this day, is to burn or otherwise try to expunge books, essays, etc. because one finds the information in them somehow objectionable; usually, but not always, according to the local mores or beliefs of the time. When this has happened, valuable contributions to the Great Conversation have sometimes been lost forever.
Although it doesn't explicitly suggest a complete physical destruction, you might consider 'efface':
FORMAL to remove something intentionally: The whole country had tried to efface the memory of the old dictatorship. (-- Cambridge Dictionaries Online)
As well as the sense of erasure, there's a medieval sense of absolution, and possibly of spiritual cleansing.
Origin: Late 15th century (in the sense 'pardon or be absolved from (an offence)'): from French effacer, from e- (from Latin ex- 'away from') + face 'face'. (-- Oxford Dictionaries Online)
I think the perspective matters for this answer. The people doing the destruction might call it something like a purge or cleansing, because they see it as the removal of something corrupt or malevolent.
Someone who values the library would see it very differently, probably calling it something like obliterating, eradicating, or expunging as Elian suggested.