The only way i can make sense of it is to use the idea that it was most likely taken from.....the Black Oil in Xfiles.
The oil itself is sentient, pretty much the black goo is shoggoth(s). The SJ's at one point could probably control it, to terraform, make their ships, cities, etc.., but over time it developed sentience and became its own "lifeforce". You could say the humanoid form of the black goo/oil is the Xeno with some of the hosts traits of course. Its possible that burning fifield and holloway was the best thing to do because even if you tried to just kill the host (gunshot wound), the goo would keep them alive as a symbiote or even just drain out of the dead corpse. Burning them is like sterilizing an infection and killing the goo.
Just like in Xfiles, the evil Aliens are the greys infected with or birthed from the black oil, and the good aliens are not. Man was created by the black oil infecting cro magnon/neanderthals and mutating him into a more "grey" like state (hairless, speech ability, brain capacity, smaller physique, etc) The oil itself is trying to take over the universe by "possession".
The oil in xfiles even takes over some worms in the artic that infect humans and make them kill each other. Its hard not to see Lindelof copy and pasted this. But i guess thats ok since they are both owned by Fox......
Knowing Lindelof, the first scene of Prometheus 2 will be the Xeno getting into a SJ ship and taking off after "mommy"