I am hesitant to dive into any of the religious symbolism, because honestly, I don't care about it.
I thought the film was pretty good for a modern sci-fi pic. The visuals were just absolutely gorgeous, and the continuous shots of the sun and related camera tricks with it reflecting off the ship's shield are some of the most beautiful sci-fi imagery I've seen on the big screen.
I think the first act was just about flawless, and I actually think its deliberate pacing (before the navigator's fuck up) actually saved the film from pseudo-sci fi action movie mediocrity, to be honest.
The spacewalk sequence and death of the pilot was handled really, really well, and I think it was probably the high point of the film for me.
The whole burned guy/abandoned ship subplot was off-putting, at least for me. It occupies a significant portion of the second half of the film, yet for some reason it still feels minimized in the grand scheme of things. Either the editors should have gone for broke and turned in a long, long-running time film in the spirit of 2001, or trimmed the fat from the first half and dropped the pretence of a grand sci-fi epic and turned in a concise, bloody space action slash-fest.
After Cappa (or whatever pretty-boy's name is) gets stuck in the airlock, I had a lot of trouble liking the rest of the film. I think it was an error to render the only character anyone has any emotional investment in completely useless. Then the ridiculous jump to the separated payload section, and the weird not-really-climactic climactic final showdown in the cavernous payload section (I was expecting to see the Ark of the Covenant from Raiders to go sliding across the pitching deck during the action sequence).
I wanted to love this movie, and liked it a lot, but it is pretty flawed.