OP, with respect, I think you're not getting the point of what the Catalyst is saying.
Sepharih wrote...
Assuming that the Morning war and/or the Metacron war Javik speaks of are meant to be examples of the impossibility of synthetics and organics living together because organics will always try to destroy them out of fear, then it actually isn't EDI or the Geth that prove the catalyst wrong, but rather it is the Quarians and Shepard who prove him wrong by choosing to co-exist and recognize the value of synthetic life.
TLDR:
Even if StarChild is right and synthetics will always rebel against their creators, his logic is still stupid.
Geth/Quarians and Joker/EDI actually can be seen as helping the Catalyst's reasoning. Part of the Catalyst's logic hinges on the idea that war and peace are not eternal; hence, there are cycles of war and peace. We have only seen war/animosity before; these situations show that peace is also an option. But clearly peace is not the only option because we have seen war. Hence we can infer that war and peace are part of some weird cycle.
The Catalyst accepts war is not a certainty but a possibility and that peace is not a certainty but a possibility. This implies that, in the long run, as all probabilities will eventually be realized after enough time, we will go through cycles of war and peace.
The Catalyst is trying to stop a technological singularity. By definition, any war after the singularity will be won by synthetics. Organics will never be able to catch up in terms of evolution and advancement.
The Catalyst assumes that since there will be repeated cycles of war and peace, eventually the synthetics will choose to end the cycle by realizing peace is only temporary and will exterminate all organics. Time is irrelevant here. Any point after the singularity means organics will be forever inferior.
I'm not going to bore anyone reading this with a long thing explaining the Catalyst's logic; see my sig for a place where I do that. I'm not saying I agree with the Catalyst; it obviously makes some leaps that can be questioned.
But the Catalyst is NOT just "killing organics with synthetics to stop them being wiped out by synthetics" and the problem is NOT just "the created will always rebel against the creators". You have to look at the idea of a technological singularity, which renders the problems entirely in a different light. Before the singularity, there is a nonzero probability organics will be superior and/or win any conflict.
After the singularity, there is a zero probability organics will ever win.
War and peace will come and go. Repeated cycles, after enough time, the Catalyst assumes, will lead to organics' demise after the singularity.