An astonishing excerpt from the Movies.com interview with Ridley Scott:
Movies.com: We had heard it was scripted that the Engineers were targeting our planet for destruction because we had crucified one of their representatives, and that Jesus Christ might have been an alien. Was that ever considered?
Ridley Scott: We definitely did, and then we thought it was a little too on the nose. But if you look at it as an “our children are misbehaving down there” scenario, there are moments where it looks like we’ve gone out of control, running around with armor and skirts, which of course would be the Roman Empire. And they were given a long run. A thousand years before their disintegration actually started to happen. And you can say, "Let's send down one more of our emissaries to see if he can stop it." Guess what? They crucified him.
Yeah. The reason the Engineers don't like us any more is that they made us a Space Jesus, and we broke him. Reader, that's not me pulling wild ideas out of my arse. That's RIDLEY SCOTT.
So how did our (in the context of the film) terrible murderous act of crucifixion end up wiping out all but one of the Engineers back on LV-223? Presumably through the black slime, which evidently models its behaviour on the user's mental state. Create unselfishly, accepting self-destruction as the cost, and the black stuff engenders fertile life. But expose the potent black slimy stuff to the thoughts and emotions of flawed humanity, and 'the sleep of reason produces monsters'. We never see the threat that the Engineers were fleeing from, we never see them killed other than accidentally (decapitation by door), and we see no remaining trace of whatever killed them. Either it left a long time ago, or it reverted to inert black slime, waiting for a human mind to reactivate it.
The black slime reacts to the nature and intent of the being that wields it, and the humans in the film didn't even know that they WERE wielding it. That's why it remained completely inert in David's presence, and why he needed a human proxy in order to use the stuff to create anything. The black goo could read no emotion or intent from him, because he was an android.
Shaw's comment when the urn chamber is entered - 'we've changed the atmosphere in the room' - is deceptively informative. The psychic atmosphere has changed, because humans - tainted, Space Jesus-killing humans - are present. The slime begins to engender new life, drawing not from a self-sacrificing Engineer but from human hunger for knowledge, for more life, for more everything. Little wonder, then, that it takes serpent-like form. The symbolism of a corrupting serpent, turning men into beasts, is pretty unmistakeable.
Refusal to accept death is anathema to the Engineers. Right from the first scene, we learned their code of willing self-sacrifice in accord with a greater purpose. When the severed Engineer head is temporarily brought back to life, its expression registers horror and disgust. Cinemagoers are confused when the head explodes, because it's not clear why it should have done so. Perhaps the Engineer wanted to die again, to undo the tainted human agenda of new life without sacrifice.