I like this take, I'm stealing this as my headcannon. It's especially interesting to think of the black goo as able to design a parasite specific to the species it comes in contact with. And the LV-223 base might be part of a former alien MAD deterrence program, similar to an SSBN or a missile silo.
I still have to watch the prequels after "Prometheus", but that prequel was one of my favorites in the series, and your comment makes me want to go watch them.