In an article behind the paywall, Baseball Prospectus ranks the Pirates first in MLB in fewest adjusted wins lost (specifically, Team Adjusted Wins Lost or TAWL, a variant on WAR) due to injury. How much this means is probably open to conjecture. The calculation itself is dependent on the quality of the team to some degree, because if your players are bad you're not going to lose many wins when they get hurt. Houston, for instance, ranked third in MLB in TAWL, but that was because the Astros were so bad that it didn't matter much which players were on the field. The Astros ranked 18th in DL stints and 24th when day-to-day injuries were included. The Pirates, however, were fifth in DL stints and third when day-to-day injuries were included, so their ranking in TAWL arguably isn't misleading.
One nice thing about the calculation is the inclusion of day-to-day injuries. With the Pirates, the most harmful time lost by hitters involved Neil Walker, who missed a lot of time while not on the DL, and Andrew McCutchen, who missed a few days of non-DL time.
The article included this comment:
I was less surprised that the Pirates performed so well in the TAWL rankings than I was by their performance on the field. Pittsburgh was the best team in baseball in TAWL in 2012 after coming in ninth in 2011, which strengthens the notion that the Pirates’ front office and administration is finally making noticeable improvements.