Agreed. Whatever the rules are, the ump was clearly wrong (as he himself admits).
The guy pitched a perfect game, so give it to him!
And there is precedent for MLB reversing calls and stats too, not only from that Yankee-Royals "Pine Tar" game, where game stats after the Ump made the call were temporarily wiped until MLB re-established Brett's home run as a stat, but that the game would be 'replayed' and 'continued' from that exact point in the game, thereby wiping out any stats which occurred afterward.
In the late 80's there were a bunch of "no-hitters" awarded to starting pitchers who didn't finish the game. They were called "Combined No-Hitters", where a relief pitcher would finish the 'no-hitter' for the starting pitcher .. the whole concept was ludicrous! In one case (I think it was my Yankees) a 'no-hitter' was awarded to a pitcher (Andy Hawkins?) who actually LOST the game on a bunch of walks and fielding errors ... but was awarded a No-Hitter nontheless!!!
MLB put a stop to all that ludicrous nonsense and completely wiped those 'records' from the books. They can do the same in this case, and really they should. The runner was OUT, clearly at any camera angle .. even the drunken guy up in the cheap seats could tell, albeit in triplicate :)