The Marvel-verse gov't is willing to turn a blind eye to the occasional killing, accidental or even purposeful, IF you are a hero who has done a whole lot of saving. After all, the Hulk got a Presidential pardon when he saved the world.
But when you do something so drastic as what Scott did, and it's effects are so wide-spread, they'll need someone to take the fall, they'll need someone to be the Villain they can make a face and example of. Scott is apparently willing to be that face, that villain, and I suspect when he comes to trial he'll tell the judge about how the Phoenix possess him and all the others, but that they need to let the others go because they didn't volunteer like he did, something like that, so that he can plea-bargain his way into being the Martyr that the cause needs and that the Gov't can have to assuage the masses.
Cyclops must have surrendered voluntary to lessen human hatred against the mutant race. In the same vein that Captain America ceased hostilities even if he had the upper hand against his fight against Iron Man.
One possible way for Scott to walk free is if mutant aggression against humans becomes uncontrollable, Captain America might be willing to strike a deal as Scott to turn the tide. Number one hero among homo sapiens superior would carry a huge clout in pacifying the mutant community