What is your theory then?
My main theory is that the story's a mess and that there is no clear and cohesive answer.
In subsidiary order, I argue that:
- The Engineers are in general peaceful. They created life on Earth and later left signs so that humans could visit them, and receive the DNA disintegrating black goo. That way humans themselves can also create life, once they meet the condition of interstellar travel.
- The black goo is produced on LV-223. Something however went wrong, possibly an Engineer who sabotaged it, (the one in the cryo) and xenomorphs or other dangerous mutations were born and killed the Engineers.
This explains:
- Why they created life and why they left a star map invitation.
- The randomness behind the black goo: It was not designed as WMD. Only as a general way to create life.
- Why the awakened Engineer killed off humans.
Only problem is the xenomorph mural, but the "men as cattle" theory doesn't solve that either.
The problems with that theory are:
- What's the reason for the star map?
- Why is the testing ground and military facility so far away?
- Waiting millions if not billions of years for a testing ground?
- Why the random and unpredictable nature of their WMD?
- How stupid were they to let this super-dangerous black goo, if it was designed as such, go rampant?