The uh... Omicrons weren't destroyed. They still exist, unchanged but in stasis for the time being. Their mirrors in Ultima Thule even went so far as to try and reactivate them, knowing it would doom all life in the universe. In fact, that was precisely why the faux Omicrons wanted to reactivate them. They want to "improve" themselves only as a means of survival, not because they in any way regret the actions of their templates. They've even said they would resume their mission if they could. In other words, barring some retcons or some really weird writing, the Omicrons remain an existential threat to everything. What's to stop them from trying to send another signal to the originals? Their reactivation means the end of all life.
We as players are of course well aware the writing is highly unlikely to take a dark turn like that. More and more, the game has been steering away from things that are vantablack levels of dark. Whatever final outcome the Omicrons get, it will somehow be something wholesome. And this is where I've taken umbrage, not at the concept of a former enemy bettering themselves. In this case it's a bunch of machines, most of whom do not even have free will to start with, being set up to undergo a profound internal change, in complete defiance of their programming. Even Omega, the most advanced thing to ever come from them (and having evolved well beyond its original programming and limitations) could never fully free itself from its Omicron mindset.
I wouldn't have taken issue with it at all if the writers spelled out how these behaviors were absolutely empty and being undertaken for purely pragmatic reasons. Faux or real, the one thing the Omicrons were programmed to do above all else was survive. Playing nice could very easily be construed in this manner, and it would make perfect sense.
And as for Emet-Selch? If the reborn Emet-Selch were to attempt something that would result in the destruction of another world, yes, at that point they could be held to account whether or not the plan succeeded. Intention matters a lot, and a good deal of what we've seen of the Omicrons indicates their intentions are still very hostile.