The destroying/reading books idea was bugging me for a bit. I couldn't remember which game had that. Then I remembered! It was angband! If you were a fighting class, you could destroy most spellbooks for XP instead of carrying them to the town to sell. Aaaanyway. Just thought I'd give credit now that I remembered what that came from.
I'd make the fragments thing a quest, so once you have read all of them, you get a little perk or something. Another thing that I think would be cool is if you could re-read the fragments any time, changing your answer to a different one if you feel like it, just in case your character has changed. I think all this would require is putting a flag in the script noting the answer(s) you chose.
I would also think that unless we're talking a single short verse per passage, there should be multiple chances to answer within each passage, making the Karma change much more dynamic. Also, agreeing with a passage shouldn't necessarily automatically increase your Karma. If I'm not mistaken, there are certain passages in the bible (especially the Old Testament) that aren't really moral.
What would be REALLY cool is if we could use recorded passages of the bible (I'm sure there are plenty of good ones out there in the public domain) and not have the message box contain the text, but a question. EG. "Was X's decision OK?"
Bible Radio?
Interrupting your combat to ask what you thought of the passage you were too distracted to listen to since 2010. 
TBH, I think that radio would be the best as far as RP goes. Attaching a quest to add more passages would be ideal (as mentioned in a recent request by csgators for More Where That Came From). Also, the crazy DJ who only speaks in bible quotes would be pretty awesome to talk to.

I am willing and able to do sound and GECK work for this.
EDIT: Duh. Just saw that this was in the suggestions box. I will start work on the Bible Radio, unless you guys would prefer the other?