Ridley said so.... but he has a habbit of misleading us.... and maybe a Red Herring.. and i am sure after some critism from Christian Community about Prometheus and the Jesus Engineer and even creation by a Humanoid Engineer Race.... upset them..
I am not sure they would go that route...
You see the way they was going with the Ancient Alien connections, is not to say yes this is the guys behind the Bible, but that the Bible, and every Ancient Culture and ideas, be that Mayans, Native Indians, Summerian, Greek etc etc they are all just a re-telling of interaction with our Engineers as far as the context of the movie...
So he may not literally mean it because we killed Jesus, he is kind of saying maybe the Bible and Jesus story is based on a actual event related to our Engineers that had been misinterpreted as far as the Bible goes... again within in context of the movie...
So basically The Engineer sent a Emisary to kind of warn us of our rebelious ways back in those days of the Roman Empire, and we well Crucified this Emisary....
Again he is maybe just throwing that out there and it may not be the case, but what he is hinting at is that YES there was something and some way that Mankind had became 2000 or so years ago that was not in the way the Engineers intended us to be... we was behaving in ways that upset them? or we was no longer subservent to them...
something trigged them to then re-set their creation....
SADLY..
This whole aspect could be now dropped, and it could be now considered purely coinsidence.