Well, to be fair, Aegis does know that humanity is capable of far more effective tools than what the Guardians have. I seem to remember that humanity has already had an AI uprising, which is why computers in Elite have less functionality than a 20th century toaster; plus, Aegis presumably knows about how effective INRA used to be against the Thargoids.
All we are waiting for now is for Aegis to get its act together and create a fleet of Mycoid-seeding, autonomously replicating, meta-alloy armoured, guardian hybrid drones to finally deal with the Thargoids.