First thing you have to remember, is they never subtitled anything David read on the inscriptions or said to the engineer, etc. The Engineer never told us it was a bioweapon, that was the Captain's assumption. The Engineer never told us it was out to destroy Earth. In fact, we didn't see Earth as the "target" until David picked it out of the star map. The Engineer did not act at all hostile or even threatened until after David spoke to it. He could have told the engineer, "I'm an artificial killing machine and all of these organics are infected." He didn't wake up with a weapon. He didn't come after Shaw with a weapon. None of the dead Engineers had weapons. Which means that there was probably no weapon on his ship.
The opening scene, to me, was quite clear. The Engineers seeded Earth with their DNA. But why the big long sequence of the double-helix deconstructing and reconstructing? Because the black goo is an evolution agent. It's not a coincidence that Shaw and her boyfriend had the conversation about God vs. millions of years of evolution. The millions of years of evolution still happened. The Engineers planted the seeds for humanity to grow... from the primordial phase onwards. And they returned repeatedly to tend their garden.
But the goo is a little too good of an evolution agent. It morphed on LV-223, probably turning an Engineer or three into a rage monster like the one crewman and that's what they were all running from. Loooooooooong-ass time later, the humans stumble in and break the containment and climate control, letting the goo ooze out and letting worm things into the room. Those worm things were quite clearly shown crawling in the goo. The evolution agent concentrate turned them into the proto-facehuggers. Being "born" into Shaw with the help of the evolution agent created the proto-xenomorph.
I posit that the Engineers were not ever actually intending to destroy Earth and the goo was not, in fact, a bioweapon. The goo was an evolution agent and they had gobs and gobs of it because they wanted to seed lots and lots of planets. Maybe, like the Asgard in Stargate, they were highly evolved but lacking genetic diversity. Maybe they just liked to play God.
David manipulated the whole thing, even Shaw in the end (because he needed someone to transport him). He got the idea of bioweapons from Shaw's dreams of how her father died (ebola).