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Your historical understanding is sorely lacking. The lapse in literacy took place only in regions of Europe which came under domination by Germanic barbarians. The attitude of the Germanic nobility was that literacy was 'ignoble', unworthy of warriors, and they thus deliberately remained uneducated (Charlemagne's court being a notable exception), and discouraged education in general.

Areas where Roman culture prevailed--the Empire in the East, and the area around Ravenna and Venice--never had a decline in literacy. I remind you that the Church was united until the 11th century, and that Ravenna and Venice were always in the Patriarchate of Rome. (Nor was classical learning lost: Anna Comnena's Alexiad, written in the 11th century, is full of classical allusions as well as references to Scripture.)

The protestants' and freethinkers' legend of the Church restricting literacy to the clergy is very hard to square with the history of mission of SS. Cyril and Methodius to Great Moravia: Greek monks, operating with the blessing of the Pope of Rome, went to great effort to give a written language to the Slavs. Hardly necessary if only the clergy (who could be expected to learn Greek) were allowed to read.

What, in fact, happened, was that in the de-Romanized lands in the Patriarchate of Rome, only the clergy and monastics preserved literacy during the Dark Ages.

I'm quite concerned with this black out of the Church's history, specifically with the oppression of literature. The dark age oppression of literature started around 494 when Pope Gelasius banned all banned heretical books and apocryphal gospels, ordering the destruction of any work of the pen not ordained. It is interesting that the Dark Ages were considered to start only a few years later (c500). Even 50 years before this, the seeds were planted by Pope Leo the Great: Here the tenets of philosophy must be crushed, here the follies of earthly wisdom must be dispelled, here the cult of demons must be refuted, here the blasphemy of all idolatries must be rooted out. Leo made it the church's goal to use its power to extirpate all philosophy, all learning, all secular science, and all competing religions... from the face of the earth. Around 590, Pope Gregory 1st denounced all secular education as folly and wickedness, and forbade Christian laymen to read even the Bible. He burned the library of the Palatine Apollo, lest its secular literature distract the faithful from the contemplation of heaven. Gregory 1st and his contemporaries even banned the reading of ordained literature by any vulgar language- only allowing the readings in church to be in Latin- something the average citizen couldn't understand, even if they were allowed to be educated to read and write. Yes, there were enclaves of literacy and free thought (notably the the Carolingian Renaissance, Bede's Historia Ecclesiastica Gentis Anglorum, & Acluin's Trivitum during the Dark Ages), but most of what you cite is actually post-dark ages, branching into the middle ages when there was a blooming of literacy and an acceptance of education outside of the church's control (spurred by the seeds of the aforementioned Carolingian Renaissance).