I honestly always felt (and still do) that the 'secret' behind why the Engineers wanted to destroy us was very simple and banal, the same thing Ridley suggested years ago - they raised their crops (lifeforms) and then harvested them, as part of a natural workaday cycle. He also often suggested the alien and other bioweapons like it were 'harvesters', like termites, equipment deployed to wipe out organisms they were tired of or even terraform worlds.
I think that's all we were to the Engineers: A crop to be harvested. No other darker motive.