Ether_Snake
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I think that moon, and the temple and tomb, are the equivalent of heathen temples. It had been built by the "fallen angels", for mankind to reach one day. God found out about the actions of the fallen angels, and punished them. The non-fallen (or repented) jockeys realized this, and to correct things went there and set up the place with goo (goo=God's will in liquid form). So if humans made it there, as the fallen angels had hoped, God would smite them. The thing is, the fallen angels were not spared by this judgement either, and fell victim to it.
The engineer at the end is one who managed to survive, and when he sees that indeed God was right, humans have even made it to the temple, which is wrong and a sin and something they failed to correct and that the humans were not even dead, he tried to kill them. He saw the situation as even worst than before: the place was set up to punish sinful-mankind if it did make it to the moon that the fallen angels had lured them to, but now not only did the humans indeed make it there, they were still alive! Basically it confirmed to him that the angels really sinned and now had to correct their mistake, but this time the situation being worst (humans have interstellar flight, etc.), he has to go and "clean" the Earth itself.
I think this would really explain pretty much everything. The invitation, the "prometheus" myth is clear there, the faith-aspect, the purpose of the goo, the way the engineer acted, why he wants to go back to Earth suddenly, etc.
