It has been a fun evening of theorizing and hypothesizing about the film, but I'm not sure if I can bring myself go much further. The fact that the basic plotting and story outline of the movie is such a fucking mess means that I'm not sure that it is worth discussing the overarching mythology, symbolism, etc. A geologist gets lost in a cave of rocks, even though he clearly has a way to map out the structure and a radio communications link to the mothership that is constantly tracking his position. A biologist thinks it's a good idea to touch and confront a brand new species of alien, without knowing a god damned thing about it. A woman fails to mention to anyone that the medpod just extracted a god damned monster from her womb.
So little effort was put into the surface plot of the film, why should I believe that there is some complex well-constructed overarching mythology behind it? Yes, there are a lot of religious, mythological, and philosophical references. Just because you can load a movie down with references like that doesn't mean there is a cogent vision behind it. If they couldn't be bothered to pay attention to very basic internal logic, why assume that they were paying attention to major themes and backstory?
To me, it's like the difference between a David Lynch film with a strange, flexible but understandable narrative (Blue Velvet, Twin Peaks) and a David Lynch film where he's just throwing weird shit at the wall and hoping something sticks (Lost Highway, Inland Empire). Can you look at all the shit thrown on the wall in Prometheus and come up with some half-baked, half-satisfying explanation for it all? Maybe, but at the same time you still have the sense that the film's creator just expects you to assemble all his intentional nonsense in a way that makes sense. To me it seems like the film and its events are left open to interpretation only because of incompetence and incoherence at the script level, not because they intended to create something that would naturally and organically have multiple interpretations.
Because it's Ridley Scott I feel like people want to read a lot more into it than is there. If this were some muddled straight-to-DVD flick without the Hollywood actors or big production values, you would just dismiss it as ambitious-but-sophomoric mediocrity and not give it a second thought.