Heres my best go at it.
Im thinking there might be two factions of "Engineers". One faction does the "creating" and the other do the "destroying".
The destroyers try to get rid of the "creators", naturally of course, and eventually succeed. During all this infighting, one creator engineer (or a team of them) secretly terraform earth. One engineer sacrifices himself...maybe even the leader....to make life on earth. His team help the humans to grow throughout time, dying off one by one. WE HUMANS are the last remaining vestiges of the creators. It might be even possible that through the randomness of nature...this leader sacrifice engineer can be reconstituted as a living human. Immortality. He is continually reborn through us which IS HIM. Just like Osirus, Jesus, Buddha, etc.
The Destroyers find out about Earth 2000+ years ago and plan to use the fire they stole from the creators to wipe out earth, so no more creator DNA will remain. The "fire" backfires before they can hatch the attack.
This might explain the Lone Engineer's Reaction to the humans. Not only are they alive and here, but they can create (David). He is furious because the only life he and his dead shipmates were able to create is the worst of the worst.....the xeno. They tried to be the creators and created the xeno. The humans tried and made David. It would explain why they worship it, not in a holy way, more like a punishment way. The same way humans might take heed to "the devil" or "the evil alien" or "demon". The same way humans make use of the gargoyle on churches and buildings. They created their own worst nightmare...and when they saw it in the flesh, that's what caused them to flee the way they did in the hologram sequence.
The secret to immortality is to do what the Sacrifice engineer does. He disintegrates himSELF.
Weyland is trying to do what the Lone Engineer's group tried to do. They are going about it in the wrong way, the SELFish way. The wrong way creates the xeno....every time.....no matter what.....its the promethean curse.
They want to destroy us because we are the last vestiges of the creators, made in their image. They couldve been doing this to every planet the Creators' seeded, and earth was just the next one, which may end up being ONE of the creators' "secret weapons".