Well, it's not just a case of protecting people. It's a case of giving into terrorism. The problem is they never bring up the option of simply covering it up. They would need a good coverup reason for pulling out of Sangala, but covering up the terrorist threat is as simple as not telling anybody. Perhaps the show really is right wing conservative after all.
On the whole, it's not an easy decision, but neither one is right or wrong. We can take care of ourselves in a tragedy. The Sangalans couldn't. No American would really give a crap, but the President is supposed to.
I'm slightly mystified by how quickly they got 1000+ planes out of the air, but they can't seem to get the rest down quickly enough. Also, since nobody really understands the magical McGuffin device, it's hard to gauge what they can do. Obviously an American pilot isn't going to fly into a building just because they're ordered to, so it's hardly a 9/11 situation. There must be some other way they can cause terra'. I don't necessarily even buy that they'd be able to get two planes to crash into each other in the sky. They'd even need some heavy math to be able to get the two planes to cross runways at the same time. That's a nightmare of a "story problem," and I didn't see anybody on Dubaku's end with a pad of paper.
Don't most of the things the device can do require manual operation? Can they shut down a power plant or do they just have codes that allow them to tell somebody to shut it down?