I will admit that I am on the pro-Krakoa side of this argument, but I have to give you kudos for an awesome post. You are right that there are elements here that make you question the X-Men, even I find the gung ho dialogue a bit different for Ororo and Scott. They actually sound like navy seals or marines which is really a different take for them.
When forming a new nation there can be a problem with how aggressive you are about settling old scores. The Americans did this when they tried to invade Canada in 1812 and got their asses kicked all the way to the White House being burned down. I am sure the Americans believed that they were going to be welcomed as liberators in Canada, the problem was that since the War of Independence the British had been trying to keep the colonists in Canada a bit happier so there was a lot of local resistance to the American intrusion into the Canadian colony. There is also the problem of how Americans were treating slaves and Native Americans, so a lot of the African Americans and Native Americans who had crossed into Canada actually assisted the Canadian militias in repelling the American forces.
History can be very complex and if we compare the state of Israel with Krakoa there can be a sense of foreboding that the country is going a bit too far against their enemies.
I still think the Orchis facility represents an imminent terrorist threat and needs to be taken down before any civilians are hurt. But I'll have to see if the X-Men go too far in their attack in the full issue of the comic.