If someone states that 2+2 = 5, should I shut up and not state that 2+2 = 4 in case some people give this fact some bad moral interpretation?
They can, but they don't. I don't understand your point. The choice you're talking about is being made. It's not because you don't like it that it doesn't exist. In any case what matters is what is actually done, not what could be done in an ideal world.
So to me the impact of methanosarcina on the environment is indeed comparable to the impact of Homo sapiens, in the sense that both are extinctions induced by biotic agents.
So, to be able to think about the world more clearly the "neutral position" is invented. There's no moral, no good or bad, there's just stuff that happens, causes and effects. And from that point of view primate, making nuclear weapons and causing extinction of the species is no different from some bacteria, who filled atmosphere with metane.
But that, again, has nothing to do with what actual author of this thread was saying. So I'm saying it only to point out that your appeal to morality is invalid. And if you'd ask me, I don't want elephants to extinct, but that doesn't make neutral arguments bad. It might be my position that goes against neutral one, but speaking is not really of much value in that case.