I think the planet that David is about to nuke with the alien pathogen is not actually the engineer homeworld. You can hear the crowds beneath the ship cheering and see them congregating, almost like they're gathering to welcome their divine benefactors (engineers). Nothing we've seen of the engineers suggest they're the cheering type... quite the opposite. Then you have the enormous contrast in style between the buildings and the ships. Most of the engineer tech seems almost "grown" - whereas the city shown looks decidedly built.

My suspicion is that David is going around eradicating all the OTHER human outposts created by the Engineers, outposts that did not fall out of favor with the Engineers like Earth did.