I've never thought about it, but how about this: Sunnydale High doesn't have a principal at the moment (Flutie dead, Snyder not yet in town). So teachers can pretty much make up their own rules for a few weeks. So Jenny, being a technopagan and jealous of Giles' collection of occult texts, decides to invent the scanning program just so she can have her own digital copies of his books.

Which means the message of the episode is "E-book piracy is evil". 10 years before Amazon came out with the Kindle, even.