I personally, see it this way.
Sure the Bungie staff have said it was a Christian allegory, but did you ever stop to think, "Maybe they just said that so as to not piss a large amount of people off?" Maybe it isn't exactly the way we're interpreting it, the way they intended it to be interpreted.
I personally think its theme is the oppression of Government and Religion.
In the game we have the protagonists, the SPARTANS, who were created by a Government, the Government of humanity, to be exact, to crush opposition to this force. In the end, their mission to purge the Insurrection fails, and a new enemy arrives, the Covenant.
The Covenant represent the Religious oppression during the Crusades. The Crusades were a military attempt to eliminate all other religions and place themselves on top. What is the Covenant doing? Militarily wiping out the human colonies one by one. If you notice, the Covenant is controlled by a Council and Prophet Triumvirate. The Prophets resemble "Space Popes" as I remember one of the staff members stating. What does the Pope and the Holy See do? Well, the Holy See is a government, the most powerful in the world, they are led by the Pope.
Vatican City has agents in every country in the entire world.
The way I see it, Master Chief brings about an 'awakening', as the first person to bring about the revelation to Humanity of the truth about their oppressors, and the Flood they are about to unleash. For example, when Cotana tells him that he is being mislead by the robot (being a machine, this could be a reference to how the media dumbs us down through machines), and that the rings could wipe out all life in the Galaxy.
The Covenant, as a result of their ignorance, unleash the Flood, and nearly wipe out humanity and everything else with it through the Halo rings. Just as how the power elite of our species is planning to, allegedly, wipe us out down to 500 million in many conspiracy theories.
I think they're true, personally, and Bungie is trying to tell us something...