The movie juxtaposes belief and religion. Eli believes in God, heard his voice. He is sincere, but the initial reaction is that he is imbalanced - just another religious crazy. Carnegie believes in Religion, but not God, and is seen as rational - evil, but rational. The ending recasts those roles: Eli is shown to be sane, and God *was* guiding his steps. Literally. And Carnegie is shown to be metaphorically blind - he could not see that he was losing the power he already had while he was chasing something that only existed in his mind.
This is also where the viewer has a choice. If Eli was blind, he could not have done all the things that he did without divine intervention or being literally super-human. Since it really doesn't feel like a superhero movie (for one thing, he dies at the end), if the viewer cannot believe that there was divine intervention in the movie the only choice is that he could see. There's no bridging the gap. It is the same with more mundane miracles. If there is no rational explanation for something good happening, the believer says that God must have intervened, because it could not have happened any other way. The non-believer says that, since God does not exist, there MUST be another explanation that we simply haven't found yet.
The filmmakers ended the movie right on the knife edge of faith. Pretty good job, too.