Personally I think Carpenter should have won it (nothing against Lincecum though, its not like he was unworthy, I just feel Carpenter was better).
Especially if you look at their pitching down the stretch. Both pitchers were pitching for the right to make the playoffs, Carpenter posted a 3-1 record with a 2.41 ERA in Sept/OCT, while Lincecum was 2-3 with a 3.38 ERA. Not shabby numbers from Lincecum by any means, but when your team is in the playoff hunt, it is time to elevate your game, not take a step back.
Adam Wainwright may have been more worthy too. He posted a 10-2 record 2.10 ERA in the second half. Lincecum 5-5 record with a 2.67 ERA in the second half