In the back game story, it states that the aliens are confused when its first completed, this is similar in SMAC to how just having the tech to build the Voice of Planet secret project increased mind worm activity and the massive amount of fungus that appears when it's complete.
If you leave the aliens alone they should calm down in a few turns, but this is a strong reason to have already completed fences.
Also, harmony in SMAC is like the Native American version of Harmony (Man is the top predator in the ecosystem.)
