I think it was a trap should the life they seeded become space farers. When the humans arrived the engineers would have taken matters into their hands to 'reset' the world. But alas there was already an incident making most of the planet and engineers dead so one engineer was defeatable.

David went and did a 'reset' on the engineers planet. Not for revenge per se, but to remove a species that didn't serve his purpose.

All my conjecture but it seems the engineers were not too happy either to see space farers, or to realise that the space farers had produced an AI which they abhored for its inherent evil. I recall that the engineer was angered primarily by David talking to him, and David was talking about immortality for his master which was probably the final straw.