I don't think it's really about "God" in itself. If you noticed, the young ppl don't even have a concept of what God is...or religion even. It can be interpreted that "faith" is what binds people together and gives them hope...especially in times of despiration like in that apocalyptic world. After all, he did die...under "God's protection". That's the reason why that villain wanted it. Because with those words from the bible comes power. He can use it to bring the "word of God" to his ppl which would like in the past, united them under his banner granting him a sort of leadership similar to how kings were. In a way, his intentions were noble, but he just went about a ruthless way of doing it. To reunite mankind in a big country, so to speak, needs the "higher power" to fear and love and follow.
I agree with you that the bad guy wanted this book for the purpose of controlling people, a tradition in religion.
Regardless of how you feel about God, this was definitely a movie portraying God's protection of an individual on a mission from God. There are too many factors that come into play, especially when you take in consideration the physical limitation of Eli. I'm getting into spoiler territory now so I'll stop.
We (the wife and I) just watched an oldie and some might call a goodie (my wife did not like it),
Clockwork Orange a highly stylized film with an interesting concept for controlling bad individuals in society, the morality of choice or immorality of having no choice all sprinkled with a high degree of sexual imagery for 1971, so much so, that originally a knee jerk reaction by the film board rated it "X". About half way through I said, hey that's the guy from Star Trek!
Age is so cruel. I say this as I look in my own mirror.