All he said was that they won't attack you.
David: "Any player can operate friendly to the aliens. The way you do it is: if you avoid killing them, and you allow their nests to exist inside your territory -- pretty much you create a sanctuary or haven, wherein their nests are safe, and you don't let people come in and kill them -- then their opinion of you will improve, and eventually it will improve to the point where they're friendly. You can tell how the aliens feel about you by the color of their units flags... if they go orange or red, they're hostile or very hostile. Right now they're sort of pale green, which is neutral, and if they go blue, they're friendly. "
Duncan: "How do you make them go blue, then? Do you have to be into Harmony?"
David: "No, you gotta have the nests active inside your territory for long enough. The opinion will just gradually kind of arrive there. And when they're blue, they will not attack you period, you can move around them... they'll just sort of exist among you, you live in symbiosis."
Duncan: "So if I put a city next to the nest, they'd probably be hostile at first, but then they'd be more friendly, if I don't attack them?"
David: "Yeah, it's kind of like making friends with a grumpy cat. You're going to get scratched a few times, but eventually, everything's going to be cool."