Yes, the run scores ... so far.
The defense would still be allowed to appeal the runner leaving early from 3rd, even though they have already gotten 3 outs. But if the defense simply leaves the field after getting the runner at 2nd, then yes - the run scores.
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"Many baseball fans look upon an umpire as a sort of necessary evil to the luxury of baseball, like the odor that follows an automobile." - Hall of Fame Pitcher Christy Mathewson
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