Here is my refined idea (innovated off that of KrikkitTwo)
Fence has 2 effects
1. Non-Red aliens won't attack the city
2. -30% str to aliens attacking the city
Quests either
Extend this to 3 tiles from city (non-Red won't enter, -30% str if they are)
OR
Extend it to your trade units from city (non-Red won't attack trade routes, aliens take 42 hp damage if they attack trade units)
I would have Orange and Yellow aliens frequently pillaging trade routes without Ultrasonic protection and Green ones "accidentally" pillaging them every once in a while.
Currently, wild aliens have only Blue, Green, Amber, and Red settings but I think Amber should be replaced with Yellow and Orange. Blue aliens will never attack any of your units but these aliens, including Shai-Hulud might accidentally get up to 2 tiles away from your unprotected city (pillaging your outer ring of improvements if tunneling megafauna, like a siege-worm). Green aliens are curious and uncertain how to react to your presence (never seeing us before in the early game or getting mixed signals from us later on). Yellow aliens are defensive and territorial but they tend to leave you alone if you leave them alone. Orange aliens are extremely defensive and territorial to the point of being hostile to you since you have proven yourself not to be trusted. Red aliens are the same as they are now, trying their hardest to remove the "human menace" from their home.
I also think that Harmony should strengthen aliens, with the highest Harmony level of any sponsor on the planet determining the added strength to the aliens (with 0 Harmony corresponding to vanilla default strengths). This can be justified by saying that as Harmony trains aliens (for Xeno Cavalry) and genetically engineers them (for Xeno Titan and Rocktopus) for their own armies, the benefit spreads through the wild aliens (hive mind for training, natural selection for genetic engineering) with the lore explaining it as either intentional or unintentional depending on the mood of the authors.
However, I think that with increased strength from Harmony, aliens should only turn from blue to orange from Transcendence towards Harmonious players. That means that at Harmony level 12 and above, blue aliens will switch to orange when the Mind Flower is constructed but still turn red against everyone else. What that means is that Harmony players need not construct massive armies to defend themselves from the very creatures they wish to join.