Good point with the bolded part.The title of Prometheus itself is a big indicator of what Scott is going for by mixing myth, science fiction, and religion and isn't really just the name of the ship although one can easily see the title applying through several layers of the film. The whole stealing fire from the gods story can be applied to the religious sect of Engineers (or Engineer to be more specific) taking the black goo (the allegory of fire), and giving life to various planets. What further cements the opposing sects for me is several things:
Sounds familiar.1) The Engineer and space ship seen in the prologue look simpler and cleaner than the ones seen on LV-223 whom look more bio-mechanical with their ships having a more menacing and horseshoe design.
Especially if you look at the hand positions on the drawings. Its like its saying "Here (the hand pointing), DON'T GO (other hand with the open palm)."2) While Ridley says that the opening scene could be of any planet I do think that the overall story he wants to tell is about humanity's relation to the Engineers both of the good and bad variety. The cave paintings/carvings seen in various locations throughout time are less likely to be invitations but warnings from the same sect of benevolent Engineers that have visited earth over the years looking at humanity's progress and maybe even looking out for us.
It's interesting that Shaw and Holloway found underlying topographical information about the engineer star system when combined but pictorially they can also be seen as potential warning messages saying more along the lines of: "We bring you warning that there are ships coming here that contain death"
Its like Paradise Lost in reverse, perhaps. The good Engineers are the ones who are "fallen" if the majority of their race are "evil" (ie into destroying, making weapons, etc).which brings me to the third numbering.
3) While I suppose the "our creations have run afoul of us" logic can be applied, it doesn't really add up when you look at the overall story. The more war like race of bio-mechanical Engineers don't strike me as careless or stupid enough just let their weapons run amok unless there were some outliers to explain this. What makes the most logical sense to me is that the events of LV-223 and LV-426 previous to human intervention were the result of sabotage by the other sect of "good" Engineers whom protect humanity and perhaps even life on other planets which would explain the star map David found having all those planets as targets and why the ships/temples on LV-223/LV-426 were in the condition they were in.
Ridley's made a lot of references to religion and literary works like Paradise Lost and Dark Angels so the bigger picture stuff makes a lot of sense when seen in the "Engineers have been warring" sort of light.
Like you I looked at online interviews and pictures and artwork (the official Prometheus website has an awesome messageboard for discussion, too), and not only do I NOW think its warring factions, I think it can be boiled down to warring religions. The one at the beginning could be about creating life, and the one at the end all about creating death. Two things cemented that for me:
1) David is more than he seems, but more on that later in another post. I think when he read that wall, it gave an inscription on the entire incubation process of the Deacon, how to create it and such. Why would it be on the wall? Because:
2) I think these Engineers, the "evil" faction, worship it as the ultimate creation of destruction. That mural of the Deacon wasn't there just because they got bored one day, that is their "deity" and I think all of their experiments has been to get to that point. One of the ideas that the poster Roquefort Raider posited here was "religious zealots who view the aliens as the pinnacle of biological evolution and want to disseminate them throughout the universe". Well consider me on board with that idea. The fact that the cave paintings on Earth even exist indicate that the Engineers, perhaps BOTH factions, came BACK repeatedly. What caused them to STOP coming is unknown, but they apparently came back a few times. The only way for the Deacon to even exist is through the sexuality of a two humans, a male and a female, which means the "evil" Engineers took some of us back for experimentation to discover that.
What if, the ship was headed to Earth, either on a kamikaze mission or to load those ampules as missiles, to make a bunch of those giant squids, and then drop the prisoners of the "good" faction down there to make gobs of Deacons? If not prisoners, then again, if they worshiped the Deacon, some of them would sacrifice themselves to make Deacons. Scott references at least once the Aztec ritual of a guy picked to be a sacrifice, and for one year he gets all the women and food and fun he wants, and then eventually he's scarified for good crops/weather/whathaveyou for the next year. If the one faction at the beginning is willing to sacrifice themselves to create life, the other one would be willing to sacrifice themselves to essentially create death.
If someone asks, "Okay, so why was the Engineer struggling then instead of allowing the squid to impregnate him?" Just because you understand the process or even worship it doesn't mean you want to be a PART of it. If he was willing to do this through either death (kamikaze) or missiles (I think the ampules can potentially be armed as missiles, given their shape), both ways take him OUT of the equation. It would be no different than asking why doesn't the Aztec leader then be the sacrifice? Cause he doesn't want to, and someone has to record all this/enjoy the "benefits" of the sacrifice.
In closing, though, you brought up something I NEVER considered but am now on board with: sabotage. If these guys have gotten creating xenos down to a science, it would not keep backfiring like it has. Also, among the pile of bodies that Milburn and Fife find, one of them, almost in the center, is the body of an Engineer whose chest has been ripped open from the outside. My guess is that one of the "good" Engineers pretended to be a "bad" one, even up to the point of getting infected, hiding it, and letting it explode out of him to kill the rest of the bad ones on that facility. Heck a few from the good faction might have done this, not just the one we saw.