Name me an instance of awakened AI in the MEU that did not at least kill (or otherwise get him/her completely out of the picture, i.e. the Citadel AI) it's direct creator(s).
They all did.
You can use example from every cycle, except the Zha'Til. Because they are the MEU's true, and only example natural Synthesis. (and only rebel against their creators when the Reap0rz come along)
Synthetics haven't proven themselves to be any more dangerous than organics. The Rachni and Krogan posed a far greater threat to the civilizations of the current cycle than the Geth ever did, and no one is suggesting some bizarre synthesis solution to the potential threat they pose. Additionally in most of the conflicts between synthetics and organics in the lore the organics have triumphed over the synthetic opponents. The Leviathans destroyed the synthetic faction that had rebelled against one of their client races, and the Protheans thrashed both the Metacons & the Zha Til.
What reason is there to accept the Catalyst's position that a potential problem of rebelling synthetics must be solved by robbing the galaxy of free will, and turning every sapient organic into some sort of partially synthetic abomination? Why not just deal with any future war with synthetics the way any other war is waged and hammer them with conventional military forces? It has worked before.
Finally, the Catalyst is no more capable of predicting the future than Miss Cleo. It possesses no special powers or clairvoyance, and the prediction that synthetics will inevitably destroy organic life is nothing more than the result of highly flawed programming by the Leviathans. Both it and they are fallible.
The Catalyst provides no compelling argument for doing anything other than shooting the tube and blasting it to oblivion.