Hadley's HopeJune 06, 2012I wouldn't be inclined to go with the idea that there was a second crew who dealt with the outburst of chestbusters.  Why would they then leave a pile of dead Space Jockeys blocking a doorway?
It begs the question, thought, what happened the chestbursters, did someone who was mortally wounded, activate a control that neutralised them (did they revert to a less harmful state? ) before dying? 
Or, were they lurking somewhere in hibernation (remember, they seem perfectly capable of hibernating for a long time, but 2,000 years might be too long... ) or lying dead,  in some part of the ship or tunnels that the Prometheus crew didn't get to? 
As for the sole survivor, I have a theory, that stems from watching the hologram replay.  At least 3, and I think 4 Space Jockeys come to the bridge, and one activates controls, showing navigation to various planets including Earth. We hear them chattering , probably briefing about their mission to bring horrible death and destruction to these worlds, and then one stays while the others leave the bridge. He seems to be preparing for hypersleep.
What I'd deduce from that, is that his part in the mission is limited to pilot and navigator, while the other three are overseeing the bioweapons experiments, being carried out by the dozens of space jockeys later seen piled up at the door. 
This is the reason that one guy survived. He was behind a big door asleep, probably completely unaware his crew was dead, until David woke him up.