No one would have given the order to shoot them out of the sky.Had the Russians put that ship to the bottom of the sea nothing would have happened.
When they (or we) do close fly-bys you take a heading parallel to the ship in question not flying directly at it. A combat aircraft flying directly at a combatant ship is considered and act of war.
With 2 F/A-18's on their ass, they would have been shot out of the sky as soon as their bomb Bay doors began opening and they changed heading to point their missiles at the ship.
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