I'm using Mass Effect AI as the standard.
And, I think Starbrat had a point, even if it's not what I would have done.
I was asking for your solution on those hypothetical issues.
I, for one, think that action would need to be taken in those two scenarios. That's to say, letting "whatever happens happens" is not acceptable. Next off, assuming they've shown not to be able listen to reason and they do plan to wipe out every other species, I would not rule out annihilating some very large percentage of their population nor biologically altering them to some end that diminishes their threat level like the genophage. Personally, I think I prefer the turian solution (bomb) to the salarian one (genophage), but I'm not sure.
Catalyst logic doesn't apply since preserving life is not a requirement here (yes, the Catalyst arguably does preserve life).
I'm not saying synthetics are invincible, or that no organics exist that are in some way superior to an AI. However, (in the Mass Effect universe) they are capable of things beyond the realm of organic life, and the opposite is not true.
Organics have to manually enter things into a computer/machine to get the desired effect. EDI can disable firewalls on a ship and vent it to space before its crew even catches on. You saw what an unstoppable force that rogue VI in Overlord was, and it required Shepard entering cyberspace -- something no ordinary organic can do -- to stop it. They can turn the machines we depend on for many jobs against us, and then we do not have many alternatives to what we've lost. We stopped the Reapers largely because they were not allowed to be the threat they were protecting against, not entirely. They couldn't just steamroll everything because they needed to preserve the sapient species, but they certainly had the ability to wipe the galaxy clean of life and sit on top of it. And organics have shown willing to fight their AI even when they cannot win, twice with the geth, and many civilizations against the Reapers. It just takes one organic to instigate the conflict, and make lots of people (maybe even all of them) really sorry.
I suppose it doesn't matter, though. Our cycle invented some sort of doomsday-device that can kill them all, so we are plenty equipped to save ourselves if that threat manifests again. I mean, defeat is still possible, but there's some sound reason to believe we've advanced far enough to conquer it and will do so (probably want to refine the prototype, though). Even the Catalyst has to admit it by that point ("... my solution will not work anymore.")