I think you might be reading into it too much. An objective person is able to separate their personal religious views from their evaluation of a work of fiction. It's not necessary to agree with something on a moral or religious level to evaluate it fairly as a film or piece of literature. In fact, coloring your opinion of a work of fiction based on whether or not it falls in line with your religious, moral, or political views is a marked sign of a lack of emotional maturity.
I just thought it was a clumsy, cliche, heavy-handed, inconsistent, and poorly-written script, which is too bad because the camera work, art direction, and overall production values were very good. Why does it need to have anything to do with religion? It's just a classic case of a strong effort by the technical direction and actors being soured by a bad script. My opinion, of course.
What's wrong with the film's story being about religion? You just said said,
"It's not necessary to agree with something on a moral or religious level to evaluate it fairly as a film or piece of literature."But then one of your complaints about the film was that it involved religion.
The obvious stance to take there would be to say that it wouldn't be The Book of Eli if it didn't involve religion. There would be no bible for Gary Oldman's character to chase, so it would have to have a different story. Which would make it a completely different movie, would it not?