Using the new data tags, you can create unusable Enchanted Books.

/give @p 403 1 0 {ench:[{id:19,lvl:2}]}

- This gave me item 403 (which is an Enchanted Book with Knockback 2) but these books can not be added to weapons or tools via anvil. The enchantment works as though it's a weapon or tool and, in this case, will knock entities back further than your fist.

Enchanted books that are created using commands should function like books that you physically enchant or get from the creative menu.

Edit: The command is spread across multiple lines. I don't know if this will prevent you from copy and pasting into Minecraft correctly.