Intelligent design vs intelligent design

If I touch on themes that have already been discussed, I apologize. We aren't sure how or why the engineers got infected, but we do know that they were headed to Earth before everything went to hell... to "unmake" us. Shaw keeps asking why, but the answer (I feel) is right there: The corpse they found in the corridor was "approximately 2000 years old". Ego is why we were to be destroyed. Civilizations all over the world paint and carve honor to the true creators, yet 2000 years ago we birthed christianity, and now we believe in and follow one god... and humans have used that one god to play god themselves. We, as a species, had reached the point of genesis. The engineers knew it would only be a matter of time before we became them... we equaled them... rivaled them. How they knew this, I have no idea. One of the many plot holes (or, for those who feel that term is too harsh, "unexplained plot elements"). One thing is for certain, Prometheus sports a lot of faith-based ideas and themes... from the christmas tree on the ship, to Shaw's necklace, to David, the over-arching plot, etc. I wish more time had been spent going over these themes, but I feel that doing so would isolate some audience members and that would not be good for business, especially when the film is a science fiction R "horror" film. Imagine if more of these themes were discussed... churches would be protesting Prometheus like they did with Harry Potter and The Da Vinci Code (... and Pokemon lol). But seriously, when they said that the engineer had been dead for about 2000 years, and then they found that they were coming to earth to start new... it just instantly clicked with me. Thoughts?