In more formal English, the question would be, "What if a missile WERE launched at the USA?" "were" is the subjunctive mood of the verb "to be", and is used when the speaker imagines something that might happen.
"at" tells us that the USA was the target. If we used "in," it would mean that the missile started from a place within the USA. If we used "towards," we know that the missile was headed in the direction of the USA, but we are not sure the USA was the intended target. The missile may have been launched towards the USA, but flew over the USA, and hit the intended target somewhere else, e.g. Mexico or Canada.