I was in the military, and I have a little knowledge of how it operates. Let's speculate that this was a US Navy ship that shot the airliner down. Maybe an Aegis class cruiser, with a crew of 24 officers and 340 enlisted. Now, you have to get ALL these guys to to forget they fired a missle off the coast of Long Island or wherever they were supposed to be. Even the dimmest bulb in the most remote compartment is going to put two and two together when they hear the news that an airliner was shot down WHILE THEY WERE SHOOTING LIVE MISSLES OFF THE COAST OF THE USA RIGHT NEAR THAT AREA!
But, you say, the government could go in and make them all swear secrecy or they are going to go to jail for life. Maybe. But I doubt it.
I don't buy it. There aren't enough black helicopters involved here.
There are other nations that have naval forces capable of firing a missle. They can keep a secret.