Is the black stuff the Engineers' chemical weapon?
When our heroes go into the vase room... "There's a mural on the ceiling which looks like it might be human, but it looks like a human - its very mysterious - it looks like a human in a form of distress - and maybe it's a human in terms of being sacrificed to the idea of this evolution," Scott says.
"Kind of rather what I call a really dangerous creation. What they've created here is really dangerous."
So, basically, the Engineers' method of populating planets - as seen in the opening sequence - is poisonous to humans.
So, they weren't carrying weapons of mass destruction to earth.