Lindelof has commented that the end of Prometheus will not lead into Alien, but perhaps a sequel would/could.This would lead me to believe that it is a "different" Derelict in Prometheus to the one we know.
Also, I seem to remember reading somewhere that in the original screenplay of Alien, there was meant to be a fossilised Xeno that the crew didn't notice.
This also raises the question of "Proto xenos", because if the Derelict has been there for thousands of years, the Jockeys must have already engineered them thousands of years in the past, does it not?They must already exist in the Prometheus universe.