That amnesty is granted based only on the genetic appartenance to mutantkind, not because some of those villains might share the same political vision than Xavier's current position.
This doesn't detract from the morality of pardoning mass murderers on this scale, and the kind of signal it sends about the kind of society the Kraked are setting up on their island. I used that example before but would anyone watching a terrorist of thousands be pardoned and welcomed into a new country thanks to his or her origin, not be outraged and disgusted by such a thing? Would a known serial killer walking out of court thanks to amnesty not cause massive public backlash? How is that not nightmare-fuelling level of worrisome? That's exactly what Sue of the FF vocalized. What are they thinking?
The politics of that choice are evident, of course. But on the ground, we saw how the people actually reacted to them, inside and outside the system. The FF were not impressed by the morality of such pardoning, and US agents were straight up against it, which is understandable. A killer of fellow citizens can now walk away from them without consequence.
That IS disturbing.
So this has nothing to do with coexistence and new beginnings if what you say turns out right, but opportunism and state pragmatism. It's understandable as a policy, but then you can hardly have people complain about the sapiens being themselves pragmatic and using weapons like Sentinels to protect themselves from this kind of rogue mutants. That's a two-way street.
And as such, they'll have to face the consequence of such policies, like other nations on Earth regularly do when their less savory policies become exposed. I also want to point out that IF the culture they are leaning toward end-up with moral standards different than those of the rest of the world, especially how already there's a discrepancy when considering the respective values of sapiens lives to mutants with that amnesty, well the alienation of them will be complete. Is Hickman aiming for that effect, for mutants to feel ALIEN to us? We'll see. That would make for both a brilliant writing, but a sad, gut-wrenching read.