I feel '97's counterarguments to "Magento was right" fall flat specifically because it centers Xavier, rather than Kurt.
Kurt's survivorship serves as the perfect anti-thesis to Rogue and Magento's (justified) anger and desire for vengeance in the wake of Genosha, simply because he does not react the same way that they do.
Kurt shares their grief but not their anger. He does not join Magento on Asteroid M, despite going through the same ordeal. Kurt would have been more than justified if he caved to despair and anger. But he did not. He still chose mercy, compassion, and hope for a better world.
Is he a fool for doing so? Maybe. But the show doesn't allow us to see his view. We don't even get to entertain it. The closest we get is "You were spared from seeing what Rogue and I had witnessed"--speech as he comforts Jubliee's anger at Rogue.
Not only that, but we completely gloss over it in favor of going back to the classic Xavier v. Magento, which feels ridiculous. Being lectured by someone who did not even witness the horror of Genosha makes any counter-argument feels so shallow and self-righteous.
Now any argument made against Magento's actions leading up to and after he scrambles the earth's magnetic field can be easily refuted with "Xavier wasn't there," but Kurt was. And Kurt still chose to walk alongside Xavier at the end of it all.
There is a somewhat similar ethical dilemma is posed in the Lifedeath comic arc where Kurt and Forge are on the snow-covered rooftop to confront a dire wraith, a skin-stealing alien that has murdered countless people in an attempt to take over their world.
Kurt asks him what he plans to do. Forge executes it right in front of him. "Don't ask foolish questions."
And was Kurt a fool? To even entertain the notion of mercy in the face of such horror and monstrosity? The comic did not say who was right or wrong in the end. I don't think it even acknowledges Forge's actions after this panel. You, the reader, are simply left to determine it yourself.
I feel '97 could have done something similar. Not to say that it couldn't maintain its thesis of "Magento was right," but it should have given more credence to its anti-thesis by using Kurt as its center rather than Xavier.
Give the viewer enough to grapple with to have them come to their own conclusion. It would have been damn good storytelling or at least made for more interesting discussion.