There are some creative ways the computer games industry used sneaky little programs that would be termed malware to great sucess. You don't have to destroy someone's computer to create security.
My favourite prank along these lines was the recent one with a game called Game Dev Tycoon, a sim game about running a games developer. They seeded copies on the Pirate Bay which were slightly altered so that you couldn't actually make any money selling your games, because of in-game piracy.
I'm sure our creative programmers could come up with something fun, unpleasant but basically harmless around ebooks. Imagine a nice little app that deleted all the vowels in the book, or that substituted words at random.
I don't think it'd work, to be honest. It's possible to embed malware in ebooks, but I think it would be easy for pirate ebook aggregators to filter out - much easier than it is for games devs, who can do sneaky stuff that doesn't trip the alarm on virus scanners.
Unlike Judy, I'm concerned that - despite what the proponents of this idea say - it will inevitably end up being used against common-or-garden file-sharers; just because everything along these lines always does. Things like terrorism, espionage and paedophilia are always used as the justification for extending control over our comms and devices, and then when they are brought in the RIAA suddenly says, hey, OUR intellectual property is really valuable too! And the law is pretty broadly drawn! Next thing you know ICE is seizing some guy's rap blog for embedding old Youtube clips and the feds are pressuring New Zealand into illegal spying to shut down a cyberlocker.
Here's another thing: remember Sony's CD rootkit debacle? They loaded music CDs with a program that silently installed malware on your machine if you play them using a PC. This malware hid itself from the user pretty effectively, and tried to thwart copying. (Remember: this was a legally purchased CD.) The mal- part of the situation (beyond the essential maliciousness of installing a rootkit without asking) was that it left a gaping security hole that a malicious third party could exploit to run botnets or, well, anything.
Malware is intrinsically a bad thing. If you are legally allowed to deploy it against Bad People, it has the potential for really bad unintended consequences for good people.