At one time, blown calls were considered part of the game, for better or for worse.
But since the ump has admitted his error and Selig has the power to overturn it, he should do so. One guy gets a hit negated, the next batter gets an out negated and the pitcher gets a perfect game, which he actually earned. No affect on the ultimate outcome of the game. I think this is an easy call.
It would be more interesting to award him a perfect game while leaving the hit on the record.
It would create a great new trivia question. "Who is the only play ever to get a hit in a game where the opposing pitcher threw a perfect game?"