Well, yes, obviously the player "observer" should not intervene. You AI actually has the slightest disadvantage in the contest because it expands faster and encounters the Faction 1 asteroid sooner, thus depleting it's forces allowing Infected a slight advantage. This was much more pronounced in the other map you had made- not so much in the organic. You also think that the fact your AI is designed to "scout" asteroids whereas Infected already "knows" the map is a disadvantage. On observing the battles on the organic map, it seemed to me that the unpredictablility and quickness of your AI often gave it an advantage in that it was able to disrupt Infected's more mechanical "train" approach. I often witnessed Infected get suckered into attacking a just-abandoned asteroid only to see your forces immediately return and wipe out the Infected invaders. Most interesting!!!
In order to truly crown the superior AI, a large number of matches on various maps would be necessary. The sample so far is much too small to come to a definite conclusion.