Is Ridley Scott trying to rewrite history with Prometheus?

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MemberOvomorphJune 30, 2012913 Views24 RepliesFor me this all hinges upon connecting two massive disparities that absolutely need to be connected.
The scenes on the boneship in Alien, in which its patently obvious the ship was carrying a cargo of facehugger pods for an undisclosed purpose.
Even as far back as my teens (I am now 30), I speculated on the connection between the space jockey and the alien pods.
It seemed pretty obvious given context that either they were collecting them, or distributing them.
(I will state for clarity that I know that the movie Prometheus does NOT take place on the same planet as the one in the movie Alien, however that point is moot, because we're talking about speculative origins)
In the movie Prometheus, it seems that the engineers/space jockeys seem to be aware of the existence of the alien xenomorph as we know it in the movies. This before we see a random chance occurrence of one infected human impregnating a human female, to create a possibly very primitive form of facehugger?
Which later manages to deposit genetic material into the body of a space jockey.
The result of course from that random series of events was a xenomorph of sorts.
Now, given the context of Prometheus, they seem to give conflicting ideas about how xenomorphs came into existence.
The mural seems to imply they knew about it at least 2000 years before the xenomorph we see in the movie, yet throughout the entire film not a single xenomorph alien as we know it is to be seen.
We see all other manner of horrors which the black mutagenic goo can create, however it seems that a very specific series of genetic bootstrapping as it were is required to produce our beloved xenomorph.
So, will it be revealed that the engineers have been pursuing some kind of nietzchean supreme being or biological super weapon, and seeded earth with humans to reclaim and use in their experiments?
Because that seems like the most plausible explanation unless of course Ridley Scott is completely disregarding what happened in Alien and generally being a total asshole and bastardizing the series.
I would like to think he would show enough respect to the original that he wouldn't attempt to rewrite history, that would be a tad narcissistic.
Prometheus is a great movie, one of the more interesting films I've seen in a while, but it is not nor could it be Alien, and cannibalizing its mythos to satisfy some kind of artistic ego-boner would probably kill my interest in seeing any subsequent movie in the series.
In short, it doesn't have to be a prequel, but they should show the original the respect that it deserves by not utterly contradicting it.
The TL:DR version of this question is essentially this:
How will Prometheus attempt to explain that according to Alien mythos, some boneships were carrying a compliment of pre-"manufactured" facehugger pods. Primed and ready to fire.
Will they even attempt that? Will they pretend that the space jockeys at no point ever genetically fine-tuned the xenomorph into what can only be explained as a pre-manufactured mass produced weapon, ready for distribution?
I sincerely hope they at least try.