The humans weren’t created to be destroyed. They were created to become hosts for the xenomorph. The engineers already knew what the end result of human infection was. The mural in Prometheus depicts a godlike xenomorph.
I believe their goal was to give a planet to the Xenos to inhabit and evolve. David knew this as well. He no doubts found libraries and scriptures that explained this to him. He merely sped up the process under controlled conditions to create the final form but was unable to reach it because his experiments were destroyed. Now he has thousands of potential hosts to refine the evolution process even faster.
He only needs to manipulate the gestation of a Xeno to create a queen in order supply the many eggs seen in the derelict ship found on LV-426 during the first two movies. The next movie will no doubt focus on Davids experimentation with the Xeno and the creation of the Queen.
At some point, David becomes a host and births the final form. The mechanical structure of the Alien we see was no doubt passed on from David since he’s a machine. Don’t ask me how. Perhaps David has some ‘bio-mechanical DNA’ used in his creation by Weiland Yutani. And most certainly wanted to contribute a part of himself to create the ‘perfect organism’.