Very, that's the kind of post that I really wanted to see in here. Read through it once, going to do so again.
Yeah I think allot of people are just accepting of what David/Shaw interpret as the engineers intentions and trying to make that fit with biblical mythology.
Of course from a human/designed by humans robot point of view it seems like a weapons facility, it was also evidently a place of worship. I think the engineers have a greater purpose than WAR. Their purpose seems to be of understanding life, and in medling with it (again fire of the gods myth) they went to far and are thus punished by the xenomorphs/plauge.
If david was telling the truth, and they where planning on returning to earth, maybe they where going to check up on us, or maybe they wanted to chill out. Maybe they thought we where ready for the next stage of "evolution" (ala 2001:space odyssey) and the black goo was intended to mutate us into them. We simply don't know from the movie.
The questions of why they made us and why they (presumably) want to destroy us are unanswered IMHO. That is why Shaw takes off in the end, to further he quest for the answers she didn't get.