I just have no idea how audiences could be expected to conclude, based only on what we saw in this film, that Jesus was actually an Engineer, and the Engineers are mad at us for killing him. Whaa?
I didn't come to a conclusion remotely along those lines, however the 2,000 year timeline suggested that something was in play that linked the beginnings of Christianity with whatever disaster went down at the Engineer's facility. And I spotted the time table synchronicity well before reading this article; it presented itself in my mind shortly after seeing the film. Ridley Scott's tendency to use religious symbology had already primed me before-hand. I was actually going to bring it up, but, well, it's here now.
The "Space Jesus" concept may have been a starting point for Scott, but then, so was the vulgar idea of an "Alien Prequel," and he tends to gravitate toward ambiguity rather than straight forward connecting the dots. The film as it is has a lot of room for alternative interpretations.
It still makes an interesting point about acts of destruction as an act of creation, and sacrifice. I've run across the cultural practices of early humans sacrificing their best individuals to the gods (or God) for the benefit of the tribe or community in some of the reading I've done exploring universal human myth patterns. For some early societies, they would set up a God-King on high to rule over them, then after his allotted reign, he would submit to ritual sacrifice in service to the community. "A King has his reign, and then he dies. It's inevitable."
I get the impression that this is a pattern of human behavior that is a deeply engrained part of our species' psychological make-up. You can fit the story of Jesus into the pattern, in a sense. I think it's still with us, too, it just manifests in marginally more "acceptable" ways. We build up the occasional political figure, sports star, or hollywood celebrity in our society's collective consciousness, build up their reputation, set them up high on a pedestal. But it's only ever a prelude to destroying them, tearing them apart. Two sides of the same coin, perhaps? On one side of it is the desire to sacrifice something precious to appease God or the gods favor, in order to benefit humanity, move us forward. On the other side, a homicidal (deicidal?) inclination towards our gods, and kings, anyone who sets themselves on high over us, or who we place up there. That's very unfortunate.
The Engineer's mutagenic liquid has been the main source of curiosity, I worked out some of it, but it makes it even more interesting as a substance that reacts to a persons intent (it works for me when I recall the idea of a variety of secret formulas that give characters superpowers in the comics, "It only amplifies the characteristics you already possess." The physical embodiment of sin itself, in liquid form, it's utterly captivating a concept. It fits with the idea I've been assuming, which is similar to what another poster suggested earlier, having to do with the nature of the Engineers and Prometheus.
Someone mentioned the idea that the sacrificial Engineer at the beginning was Prometheus. But that liquid they use, they all don't have a good handle on it, do they? I like the idea that the Engineers as a species are an entire race embodying the Prometheus ethic; it's fun to think that they acquired the liquid from something else; and their reaction to us is informed by their encounter/s with whatever originally possessed the liquid (Do they think we will eventually want to kill them, because they know how they felt when they were in a similar circumstance: they met and wanted to kill whatever their father/god/maker was and steal his technology, too? They already tried it themselves, to an extent?). We only see male Engineers. One possiblity that occured to me was what if they are cursed in some way, their life-cycle is symbiotically/parasitically linked with the Alien/Xenomorph life form. The Engineers are cursed to being torn apart from inside as part of their joint life cycle with the Aliens in punishment for taking the liquid (like Prometheus was cursed to being perpetually torn apart, healed, and torn apart in an endless cycle of tormented life for stealing fire).