Allegory in the Ending

I'm not sure this is what I would call an allegory if I understand the word's meaning that is. I think one of the obvious themes of the movie is exactly what you said. I think you have the idea of science vs religion from the very beginning of the movie with shaw's dream. You also have the theme of creator vs its creation two fold with engineer > human > android. I think of an allegory being something like the lion/jesus in the lion the witch and the wardrobe. The science vs religion I think I would classify as the actual theme that they drive into you like a truck from the very beginning. Even the first scene with the engineer disrobing at the waterfall and sacrificing himself has a very religious tone to it.

Who's the dude who gives him the elixir? Did I miss that?

Yes, halfway through the film I had the strong feeling that these two polar opposites would be paired together for, and set up for the sequel. David admired the Space Jockeys "Surely a superior species" and does not think highly of humans and their irrational beliefs (look how often he mocks Holloway and Shaw's beliefs, including taking Shaw's crucifix in the medical bay, - which he puts on a table in a plastic container, but for no apparent reason, when she returns to the Space Jockey's ship to find David and his body a few feet apart, the first thing she asks him is where her little cross is... (surely she should expect it to be part of the debris from the Prometheus) and David has it in the pouch of his utility belt. He thinks her quest for answers to "why" are irrelevant. He has no purpose other than to serve and doesn't know freedom, whereas Shaw seems to view the "why question" as her main motivation, even above the desire to wipe out the threat to earth, which she leaves to Capt Janek (it's implicitly agreed in her quarters that she'll go to the Space Jockey to ask "why"and he'll do anything it takes to make sure that the crap doesn't go on his ship back to Earth) They make a contrasting pair also because David has killed without remorse, to fulfil the wishes of Weyland... he seems to have chosen to infect Holloway, because Holloway was drunk, and available, in a common area, and perhaps he took some pleasure in it, due to Holloway's repeated insults to him, but it seems unlikely he would have killed him for personal reasons. Shaw, on the other hand, doesn't kill anything in the entire film, although she assumed she had killed the squid thing that was extracted from her. She doesn't personally kill the "Engineer" / "Space Jockey" but opens the door to let her "offspring" do it instead.

@Hadley's Hope Shaw caused everybody to get killed just because she wanted to pursue her hunch... and btw she tried to kill her "son" and she did kill the engineer

@Arkadine [i] Shaw caused everybody to get killed just because she wanted to pursue her hunch[/i] That's not murder, that's naive and reckless at worst. In fairness once they got there, they could have avoided most of the deaths. Milburn and Fifield's deaths were entirely contrived, stupid and avoidable. (and there are several plot holes piled one on the other, leading to their deaths) Holloways death was a result of David's treachery, even though it is Vickers that burns him up. Wallace and Byrnes and Davis are killed by Fifield also because of contrived stupidity having seen Vickers toast Holloway to enforce quarantine, they casually lower the door, without a radio check to ask Fifield if he's okay, and the ships camera shows him in a position you'd expect if there were landmines on a 'Twister' mat, yet neither the captain nor the cargo bay crew pay much attention to that. Dr. Forde, Jackson and Weyland are all killed for waking up a giant Extra Terrestrial being whose mission, apparently, is to fly to earth an wipe out all humans. Janek, Chance and Revell choose to kamikaze to stop this, (which wouldn't be necessary if Weyland and David would simply let sleeping sociopathic Space Jockeys lie uninterrupted in their stasis beds. Some others also die in that crash, perhaps unaware of the Kamikaze run - some orderlies and personal security for Weyland, who may have been in the 2nd Lifeboat, unknownst to Captain Janek. And Vickers dies because she opts for an escape pod, rather then being ejected with her lifepod, and thus has to run away from a rolling ship, and doesn't think to run off to the side.... Did I miss anybody? [i]and btw she tried to kill her "son" and she did kill the engineer[/i] I said she didn't PERSONALLY kill it. I know she knew that it would be attacked when she opened the door. My point is that although she at one stage holds an axe, we never see her do any fighting.

If you're looking for an allegory, dig this. At the start of the film, the first (seen) engineer drinks a brew specifically designed to seed a barren planet with his (one would infer carefully) parsed DNA. In this sense, he's the progenitor of all life on earth. This means that the engineers see a kind of honor in death that begets life (because surely they could design a surrogate for such a donation otherwise)...so it is desired. At the end of the film, Weyland risks all of humanity (for whom he presumably worked all his life) waking the Engineer for his own personal gain at the end of his life (extension of his personal life, rejuvenation of his personal body, or perhaps ending his personal curiosity). This is the desperation of a made thing who views his own personal spark as the most precious. It is not the perspective of a maker, an engineer, who has near total mastery over the making or unmaking of their life (per the beginning). However, when the captain, who doesn't care about anything in particular, is willing to kamikaze his ship containing his one and only personal body into the Engineer's craft, that is transcendent of personal, aka desperation of a made thing who views his own personal spark as the most precious. And it might explain why the Engineer didn't shoot the Prometheus down immediately or perceive it as a threat until it was too late; they don't expect it.

@Dan 321... that's good. And look at who else is having the big discussion around the same time -Shaw and Janek. She is willing to risk her life to get the answers to why - but she doesn't want to risk anyone else's life... unlike Weyland. Janek doesn't care about the answers but wants to preserve life. Also, David - who has no philosophy and we assume isn't all that bothered about having his head pulled off by the Engineer, nor about having his creator killed, or being threatened by Vickers. These may all affect his ego, which seems to be growing, but not his sense of 'purpose'. To him, shooting hoops from a moving bicycle seems more productive than pondering "why".