Interesting.
We know there are lots of SJ suits/bodies laying around. One in the ampule room, and then there was another image in the trailer of a tunnel with a few laying off to the side.
Three of the sarcophagi in the SJ control room look to have been "bursted" from the inside out. You can see it on a hires image of the picture of where david is crouched at the SJ control chair.
Perhaps by the time Prometheus lands, the party in SJ central is well underway. We potentially have dead jockeys laying in rooms and tunnels, bursted sarcophigi, and that Giger Mural has to be more than something pretty to look at. I'm wondering if some SJ creation got loose, and wiped them out. In the process of integrating their DNA, they became sentient and learned how to use the SJ technology. Once the humans showed up they discovered a world full of beings to use as incubators for reproduction.
The SJ we see in the movie might actually be trying to stop them and not wipe out humans. Far fetched I know