First of all, as soon as Atlanta's manager came storming out of the dugout, instead of a long heated argument, the Umpire could have just said "hold on, Freddie... we're going to take a look at it", and calmed everybody down. Because changing the call would not have changed where any of the other runners would end up, it could have been reviewed and changed. (Remember, on an infield fly the ball is live, and runners can advance at their own risk - which they did in this case). And then they could have waited a couple of minutes to get the ruling from the "instant replay Umpire".
Would the ruling have changed? I don't think so (*). By definition, it WAS an infield fly. Note this comment on the IF rule:
On the infield fly rule the umpire is to rule whether the ball could ordinarily have been handled by an infielder—not by some arbitrary limitation such as the grass, or the base lines. The umpire must rule also that a ball is an infield fly, even if handled by an outfielder, if, in the umpire’s judgment, the ball could have been as easily handled by an infielderAll the conditions were met, and off the bat it may not have been "ordinarily handled by an infielder", but by the time Kozma camped under it and had his shoulders square to the infield it was. So, the ruling would not have changed, but the fans would not have had a reason to throw debris towards the Umpires on the field. They didn't make the final call, someone else not on the field made it. The delay to the game would have been shorter. Instant replay would not have made the Braves any happier in this situation, but at least they wouldn't have felt as cheated.
(*) I actually believe that if no infield fly had been called, the shortstop would have made the catch, and the situation actually helped the Braves as their runners advanced one base. From the replay it appears that Kozma is under the ball and all of a sudden he gets out of the way. Why did he do that? My speculation is that he heard something, and assumed it was Holliday calling him off. Likely, he heard the left field umpire, call "infield fly, batter is out", and since players are not accustomed to playing with umpires in the outfield, he did not realize that was an umpire talking.
Here are couple of links that corroborate my thoughts:
Right call by rule
Call helped the Braves
On a separate point, the intent of the IF rule is to prevent the defense from turning a cheap double play by intentionally not catching a ball, while the runners aren't advancing to their next bases. However, the wording of the rule does not specifically talk to this intent. Maybe the rule could be changed? Adding a clause to not only say that it "can be caught with ordinary effort", but also that "and if it is uncaught can give the defense an easy way to turn a double play", would turn situations such as this one from an infield fly situation to not an infield fly situation.
For reference, here is my "Get the Edge" page on what players should do on an infield fly.
As always I welcome your thoughts.