The last post in this thread was awhile ago, but this thread is in the "Top Forum Topics" list, so it probably gets alot of traffic, and I wanted to drop some input.
I'll start out by saying that I'm an atheist (and anti-theist, I guess), and the Christianity/Halo parallels stick out like a sore thumb. They were very obvious to me. Although Halo does this, it also shows the protagonists (Humanity) as secular, with little mention of religion, with few exceptions(fairly certain Johnson is religious, and alot of the Marines will shout God's name in vain if you try and run them over with a Warthog lol). One of the main antagonistic forces is a dogmatic theocracy. The Covenant is, as you all know, entirely religious. Infact, apostasy (leaving the religion) is heresy, and probably treated with execution, so is being an infidel, not unlike past and present monotheism (Christianity a bit back, Islam then and now). The Elites and other Covenant Separatists abandon their religion twice (once on joining the Covenant, again when they leave). This may be showing a kind of weakness with theocracies and it's followers.
Another few points:
Because Bungie is an American company, it's probable most of the employees are Christian. In making a science fiction game universe about alien spieces, spanning millions of years, touching on both human and nonhuman evolution many times, Bungie is showing that in the very least, it's not made by "Bible literalists", so that's very good. To me, Halo seems more like a normal, secular game which borrows heavily from Christian mythology for artistic reasons. Also, I think I read somewhere that Joe Staten studied religion or his dad was a priest/preacher or something like that, so that's probably where it all comes from.