[Spoilers]Theory for our reason to be exterminated

I haven't come across a movie that made me wonder more than get answers so far. I have been thinking a good amount on the movie and have come up with a possible reason for why the engineers are out to exterminate us. If anyone knows of info contradictory to debunk my theory feel free to contribute. The one given thing I am assuming is that the black goo is a form of advanced bio-engineering agents (and the general consensus is that most people agree). The engineers also terraform planets and seed/create life with this. Over time, one one planet this evolved into humans. Perhaps at first they nurtured their creation, trying to explain where they came from. Perhaps, through many, many years humanity evolved and the black goo's effect on humanity also changed. This is hinted in an interview with Lindelof regarding what changed between the cave painting time and modern day. This unexpected mutation of humans creates a formula where the black goo human + another human = the trilobite. This was unintended, this trilobite infects and causes the xenos we know. That is what the engineers in the holograms were running from, xenos, and they are returning to earth to perhaps stop humans from spreading across the universe or where ever they seeded the black goo and spreading the xenos. I could be wrong but this popped into my head upon contemplating the movie. Edit: I just realized that someone found that screech when they start the hologram of the engineer's running matches the screech of the deacon alien at the end. This confirms my suspicion that that is what they are running from. I am really liking my theory that the engineers created us, and we are now the link that is creating the xenos, and they are going back to wipe us out since they made us and the we can cause the xenos. That is why the first engineer is kind of compassionate at first, we made you look at how far you have come, but this is how it has to be. The only thing I can't figure out is this seems to go against Scott's idea that the said multiple times that these ships were specifically used as carriers to deploy the eggs to clean up planets. So I enjoy my theory but it doesn't look like it is holding up.