Hey guys I just had an epiphany, in my view this makes more sense than anything has yet to come up with!
When they enter that preservation chamber they see the giant head and shortly after the alien mural which so just happens to be in a crucifixion position... What if Jesus actually was an ambassador sent by the engineers and because he was crucified they decided the human race was no good and decided on the re creating the black goo to "start fresh".
This makes complete sense with the 2000 time line and the massive religous overtones the film has.
You could argue "why didnt they just have a mural of jesus then?" answer? Because that would be as corny as f**k! Majority of people would cease to take prometheus seriously after that and it would be panned by critics and religous organisations alike.
So reason for alien mural? Because the alien symbolises death. Since they crucified jesus there would be a great irony in having death up there, effectively symbolising our fate!
Clearly the giant head is also a symbol/figure that the engineers worship, they aren't just going to put auntie hildas cousin John twice removed on there.
To me the alarm bells ring clear, giant head = god, alien mural in a crucifixion position = jesus being crucified and lastly the 2000 year time period this a makes sense.
Its also clearly we was on a relative good terms with the engineers with the cave drawings spanning tens of thousands of years and suddenly it all went suddenly wrong 2000 years prior.
I am not some religous nut, im not even Christian however these reasons make the most sense to me and since religion and believing is plastered all over this film it makes so much sense, they could of just stuck a jesus on that mural but if they did I think the majority of the audience would start looking eachother confused or just plain laugh as that would be totally corny, I know i would of.
It would of made the plot too obvious and would of plain just made bad story telling.
Plus the allusion to all this seeking for answers throughout the film and the open ended ending alluding to a sequel it just makes sense!