The Engineers created us in their own image. I think its the merging of spirituality and science. They know that they are playing with dangerous forces by trying to create life in their image but its how they live.
The Ancient Aliens theory basically says giants from the stars created ancient man and played with experimental forms of life, and in some cases wiped humans out because they were unsatisfied with them. It wasnt until God stepped in and kicked them all out that for the most part it stopped. Lots of ancient cultures share this sort of story if interpreted as such so its not really a stretch. It all just comes down to the height of your hair and what you want to believe.
I think that this fits with Prometheus in that Engineers would seed life as a sacrifice to God, heck many ancient civilizations sacrificed the crap out of themselves for their beliefs so maybe they picked up the habit from aliens. Their scientists would monitor their behavior and once things got out of hand they would wipe out life, maybe by dropping Xenobombs or by flooding, or maybe both... you do have to get rid of the Xenos after you get rid of the humans right?
Another reason for wiping out humans over and over could be that maybe not that many planets can actually support life the way the Engineers intend. They would have to keep re-using the same places over and over for the ritual to work. They didnt exactly pick LV-223 because it was a fantastic place for life to breed.