Let's start off with a quote from Beyond The Box Score, one of Sports Blog Nation's top baseball blogs. For reference, "The Book" is a baseball book written by Tom Tango, Mitchel Litchtman, and Andrew Dolphin. "The Book" is widely regarded as one of the top statistical books amongst those who follow new-age statistics.
The Books says the #2 hitter comes to bat in situations about as important as the #3 hitter, but more often. That means the #2 hitter should be better than the #3 guy, and one of the best three hitters overall. And since he bats with the bases empty more often than the hitters behind him, he should be a high-OBP player. Doesn't sound like someone who should be sacrificing, does it?
Basically, the second hitter in the lineup is more important to run scoring than the third hitter. Most second and third hitters bat in similar situations, but the second batter comes to the plate more frequently over the course of the season. The second hitter being a contact hitter who can move runners over is a waste of an extremely important batting position. This mentality is extremely outdated, especially since a number of tests have been run on the value of bunting runners over, with most of the results pointing towards it being a poor decision.
I doubt the is the actual reason for Jason Heyward batting second, but it is the correct decision -- even if it is accidental. Heyward's .400 OBP is incredible and it should remain in the top few spots in the lineup. The problem most are having with the lineup now is Martin Prado's lack of production in the third spot. This likely has little to do with him batting first or third and more to do with him suffering from an inevitable decline in numbers, pushing them closer to his career averages -- his rate stats are now extremely similar to his numbers last year.
The third spot in the lineup is actually much less important than many realize. They come up to bat less frequently than the second hitter but seldom have runners in scoring position for run scoring opportunities. Here's another quote from that same Beyond The Boxscore article.
Even when Prado is slumping he is still one of the top five hitters in the lineup, but he is closer to the bottom of that list. He is actually the perfect fit to bat third for this offense, according to The Book. Derrek Lee and Brian McCann have more power potential, while Jason Heyward and Omar Infante have better on base potential, at least while Infante's average stays inflated. Lee has not been great for the Braves, but he has been better than Prado as of late.
Again, I highly doubt that Bobby Cox and the rest of the Braves coaching staff is deciding the order of the lineup for these reasons. Even so, that does not mean they are incorrect for lining the batters up this way. Traditionally, Heyward would bat third and either Martin Prado or Nate McLouth should bat second for the time being, but according to most statistical analyses, that would be the incorrect decision.