They were wiping out a mistake, an abomination. Did you not watch the film?
Engineer suicides in a ritualistic fashion on a planet with no intelligent life, one strand of DNA survives in the water, from this strand of DNA we evolve (As is our supposed actual creation). Years later they realise that we exist, and are going to get rid of us, as we in there eyes are blasphemous, unwanted creations, did you not understand why the Engineer flipped out when David started talking, he was offended by the presence of them.
The biological weapon wasn't just for us, it is their way of extinguishing life, it adapts to the environment it is placed and eradicates all other life. Saves the engineers getting their hands dirty.
The engineers are biologists in a lab, but instead of being a room, it's the universe and instead of having petri dishes they use planets.
nice post, did you get that from jsut watching the film??? still the humans do not know any of the above information.. they just guess ...