I don't know, Scott sure seemed intent on implying that the Engineers remained active shepherds of humanity until about 2,000 years ago, when they abandoned us because we were dicks to Jesus (we'll leave out the Bible-ey part where Jesus wanted to sacrifice himself and had a human family, and how it would probably be noted somewhere if he was a 10-foot tall bald alien bodybuilder with pearly white skin and black eyes, but I digress).
That's after the film had already come out, so it's not some early idea which he abandoned later on. He didn't include in the film because it was "a little too on the nose," but clearly he envisioned the Engineers guiding humanity until we rejected them first, and the cave paintings reflect that.
Movies.com: You throw religion and spirituality into the equation for Prometheus, though, and it almost acts as a hand grenade. 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?
RS: 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, “Lets’ send down one more of our emissaries to see if he can stop it. Guess what? They crucified him.
http://www.movies.com/movie-news/ridley-scott-prometheus-interview/8232
That's after the film had already come out, so it's not some early idea which he abandoned later on. He didn't include in the film because it was "a little too on the nose," but clearly he envisioned the Engineers guiding humanity until we rejected them first, and the cave paintings reflect that.