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In the insanely improbable event that the intercept accidentally shot down the unidentified aircraft before realizing it was a civilian airliner, then it would have been pilot error for not following rules of engagement or, possibly, a flight controller or flight commander error. There's zero reason for the U.S. government to turn an individual mistake into a huge incident by trying to cover it up. Also, there are many examples of the U.S. military making such mistakes and NOT trying to cover it up.
Including shooting down an airliner. No coverup.
Carrier group is even less likely to shoot down airliner. In middle of ocean or crowded area like South China Sea, carrier group probably doesn't have its defenses on alert. It has fighters that can intercept and visually identify aircraft. In the middle of ocean, there is plenty of time to react. There isn't the hair trigger in middle of war zone that led to Iran Air Flight 655.
You'd be very wrong. There are hundreds (thousands? tens of thousands?) classified missions going on all the time involving large amount of people. And aside for the exceedingly rare whistleblower, all of them are kept secret for decades or more until they get declassified (sometimes never).
(Not trying to give any credibility to the previous comment, just commenting on how effectively governments keep classified secrets.)
Not many of them involve murdering an entire planeload of civilians.
You of course don't know that, not having access to compartmentalized top secret material.
If you did, you couldn't post here (or anywhere) about it.
The US has vast intelligence and military resources, but resources can't create operational miracles. Disappearing a civilian airplane and keeping it disappeared would be such a miracle.