I'd argue it wouldn't set a dangerous precedent:
(1) This is obviously such an extraordinarily rare circumstance (though if we keep getting perfect games like we have been maybe not so much anymore

)
(2) Reversing the call would not effect the outcome of the game; it ended with the next batter grounding out, no runs were scored after the play, no other hits, just the next hitter grounding out to third.
(3) Because of (2) there is no effect on divisional standings, playoff positioning, etc.
(4) Joyce admitted culpability.
It just boils down to a change in the box score in an bizarre and rare moment, and nothing else. You can make it one time deal, and no one will be that upset because of events leading up to it. Or, if you only apply to games that meet the criteria: (1) Historic moment; (2) The game ended on the next play; (3) Didn't change outcome; and (4) No effect on the standing; you'll probably never have to apply it again.
Granted, Galarraga will be more immortal because of this, and it will always be talked about as the only 28 out perfect game. But I still think Selig could reverse the call, and not jeopardize the integrity of the game, with all the public support to reverse the call, he might actually save some integrity.
On another note, Selig managed to say absolutely nothing about instant replay with a lot of words. Unsurprising, all things considered, it'll probably be tough to come out against instant replay now. It will be a fun off season!
-nobody