Keith Olbermann has some good perspective on this matter, which we mentioned here, where an umpire made an admittedly-bad call and cost Detroit Tigers pitcher Armando Galarraga a Perfect Game. And for all the booings and cursing at that ump, Jim Joyce, he's certainly being a mensch about it and owning up to his error.
I can understand the reticence of the Baseball Commissioner to not start a precedent of overruling umpires…but it has been done before and in this case, it in no way would affect the outcome of the game. Also, the umpire who made the call is asking for the reversal. Seems to me the game itself is diminished if it so favors a strict interpretation of some rule over simple honesty.
[P.S. Added a bit later: I should have added that the pitcher, Armando Galarraga, has also been a fine gentleman about it all. Also, I fixed a link that didn't link.]