I mean, it absolutely is as bad. There's no moral or ethical reason the "main" reality has primacy over the others. Only the utterly amoral and circular logic that the "main" reality is somehow "above" the rest.
Not sure where you're getting "... that the 'main' reality is somehow 'above' the rest" from, but in any case, it kind of boils down to, either the other realities get killed, or all realities get killed. Those realities are destined to be destroyed. I mean, I'm assuming they're going off the same kind of plot as the comics when it comes to the convergence events, where the multiverse is being destroyed as one reality crashes into another in a domino effect of Michael Bayplosions. That's what provides the heroes with a plot and purpose. Stop the destruction of the multiverse by stopping the convergence events without killing everyone else off.
Sure, Kang isn't being very heroic, and there are probably other ways to stop the convergence events other than killing off other realities, but maybe he doesn't know how. Yeah, he's a smart dude, but he's one smart dude who teamed up with a smart Janet who was smart enough not to tell her smart quantum realm observation device building family why they should leave the quantum realm alone and expect they would just accept her reasoning that they should leave the quantum realm alone for no other reason than she just said so. I don't think it would be too far of a stretch for her to follow along once Kang explained his reasoning.
I guess if you want to have a moment of morality, you could go along the lines of what they did in the comics where Captain America refused to destroy the earth of another reality in order to save the main Marvel reality. He ends up getting his mind wiped of all memories of the Illuminati, gets them back, and then fights Iron-Man to the death of the multiverse. Reed Richards builds a reality life raft, and Doom becomes God King Doom, one of the awesomest looking versions of Doom. I don't know if anyone has tried to create a God King Doom costume for a convention, but that would rock.
Also, who gets to pick what the "main" reality is, and was it always the "main" reality or is it simply a long-ago branching of some other reality?
I'm going to go with the writers. At some point in the comics the 616 universe was deemed the main Marvel reality/universe/ham sandwich. The MCU may have a different designation for the main Marvel universe, so in that case, the script writers get to choose. At the end of the day, it's a movie and not real. Which and/or why a particular universe was designated as the main universe and who gave it that designation, and what authority they had to do so doesn't really matter. It's just done for the sake of the story.
