So it could be the xenomorphs using the genetics of the host playing out as they seem to do. If it is indeed a Queen then this one coming from a Space Jockey would have some differences from the one that came from Ripley (as that one seemed to be a standard chest buster.)
I'd read some talk about something bursting out of the Space Jockey at the end so maybe this explains the Queen in the second film. The rest of the aliens could be from the eggs found by Kane/the Jorden family. Eventually eggs could be moved from the derelict to the atmospheric processor or the Queen lays new ones. Either way bad news for the colonists.
Is this film as open ended as you'd read? There seems like some potential for new prequels and have them lead into Alien. One idea could be getting a recording of the Space Jockey transmission then ship being programmed to look for similar from then on. Captain Dallas mentions the Nostromo computer being programmed for certain situations. Now with Prometheus we can at least theorize that the Company knew what to look for.