I've watched the director's cut, and gone through ti a few times myself. The overall thing that I got, was that it has rather general meanings...
Yes, there is the Chris and God theme, but also, if one compares it to 'The Stranger' by Camus, it resembles the exostencialst (sp) views and themes shown there.
So, what should you, or I, understand the movie as being about, and how should we thusly view it? No real answer, you would have to ask the director/writer. However, what I did, and what I personally think is the most interresting way, is to view it from both angles, getting different meaning from each. Either way, I think you'll come away saying, 'Damn, that was a good movie!'