One way to make this kind of thing give good or bad karma is to give the player the option of either destroying or distributing copies by taking them to different NPCs (say that Brotherhood scribe at the library, and that slaver at the Lincoln Memorial) or activating a printing press/furnace. I dunno. The possibilities are many. If you applied this to all books, including those that are mostly destroyed, it would give some people a reason to pick up all of those previously useless piles of stuff.
Adding a bible in would be fine with me, but I think that a more appropriate effect of reading it would be a disposition increase with certain factions and a decrease with others. Another interesting idea is to have fragments (as mentioned) that you can read that give you options like in the GOAT, essentially choosing what your character thinks of the passage as it goes along. If you choose to agree with the passage, you gain Karma, if you choose not to, you lose it, and if you are neutral about it, you gain XP (or lose/gain karma, depending on your current disposition, to move you closer to the center of the scale)?
Anyway, just my 2 cents. Very interesting original idea, BTW.