I think the idea that the reason the engineers want humans dead is because humans are already fighting them makes sense.
1- Engineers were friendly, created life. Self-sacrifice = good, so they are good guys.
2- Humans had contact with them, and were taught by them as indicated by the worship and star map.
3- The star map doesn't lead directly to their home, it's their "location", it's a big area. The moon just happens to be one place among many in that general area. The "home planet" of the engineers might be in that area, not extremely further away. This would remove the issue of "why invite them there, when they were on good terms, when it's actually a military installation?". They invited humans to their home world's "system", not to that particular moon.
4- Humans, presumably, did something wrong around 2000 years ago. Engineers changed their minds and decided to kill the humans. They create a bio-weapon, using their life-making-goo.
But something attacks them and foils their plans. There is no indication that the engineers were attacked by their own creation, which is still all stored in pods, albeit in an old decrepit ship. The head they brought back in was from the room with the bioweapons, so of course it was infected. The pile of engineer bodies looked like it had been made by someone; it looked like a scene in a movie when bad guys pile up the bodies of their dead enemies. The hologram memories also never show any signs of what the engineers were running from, and they didn't look armed. The dead bodies showed no signs of having been killed by weird-ass black-goo aliens.
5- The reaction of the engineer when he sees the humans is panic and attack and trying to flee with his ship, as if those humans could be an immediate threat to him (I wonder what David said).
6- The girl leaves to find out why the aliens changed their mind. Clearly the "why" is key to the sequel, and presumably it would involve a "is it the right thing or the wrong thing for them to do?".
So all of this leads me to believe that, if you tie it to the title of the movie: somehow, humans got access to the "fire" of the gods a long time ago, either given to them or stolen or whatever, and turned against the engineers (ties in to what David kept harping about directly and indirectly about "people wanting their parents dead"). So I think the holograms are showing those humans attacking the engineers, it's a space war, and this just happened to be a military facility of the space jockeys that was attacked by humans.
There can't be a sequel set in space with Shaz and David as the only humans, so expect ancient human-race with space-alien tech VS space jockeys for Prometheus 2, and hence the explanation why humans "have to be killed".
Maybe
