I think LV223 was their WMD delivery facility for our sector in space. Think of space as an ocean and a planet like a submarine. I'm mean honestly, no matter how peaceful one chooses to live, there is always the risk of someone else trying to kill you. I wouldn't be surprised if over the eon's engineer societies lost touch with each other yet still kept some sort of "on the ready, self defense" force intact.
In Alien the engineer sent a distress call saying to avoid the planet it had crashed on. It wouldn't be odd if the same transmission was sent after the catastrophe on LV-223. The reason the Prometheus didn't detect the message was because they weren't aware of the engineers communication techniques. Such as the snowy holograms. I take that snow to only mean that our eyes were not designed to see the entire picture. Now why the Covenant could detect it? It's been ten years, perhaps the people of Earth made upgrades. I don't know.
As far as sparing us, it is clear that the engineers made at least 2 trips back to Earth after the events of 2000 years ago. Which can only mean one thing. Hawaiians are Engineers.