FanGraphs.com and Baseball-Reference.com calculate WAR in different ways, but both rate Bourn as the more valuable player since 2009:
FanGraphs WAR, 2009-2011
Baseball-Reference WAR, 2009-2011
The differences in value primarily come from different methods in evaluating fielding (FanGraphs likes both players' defense better than B-R).
You don't have to agree with or even like the WAR statistic. It's just a tool -- a very good one, in my opinion -- in evaluating player performance. I think the main confusion or disagreement comes in understanding the position importance. Bourn is compared to other center fielders; Pence to other right fielders.
Honestly, I wouldn't have guessed Bourne was the more valuable player. So as a Braves fan I'm happy the numbers bear that out. We desperately needed a center fielder and a guy that can get on base and run well when he does. The Phillies needed some power in their lineup. But when you also consider what they gave up compared to what the Braves gave up I think the Braves got the better deal.
This analysis makes me think of Dan Uggla, the Braves second baseman who was traded for and given a big contract. Uggla's value was that he provided a lot of power from a position that usually didn't come with a lot of power. Though he trades that power for below average defense. But the Braves needed power. And he should have provided enough of it to be a valuable second baseman like he was in Florida (averaged 3.9 WAR in his five years there).
The problem is that Uggla was terrible for the first half of the year. From getting on base (which is something he has never done all that well) to hitting for power, he was bad. But luckily the Braves' pitching was so good that it didn't hurt the team too much. Since around the all-star break Uggla has turned it around and is hitting more like the player he was in Florida. He has a long way to go if he wants to make up for his first half of the season. Actually, he would have to add about 3.5 WAR to do that, which would probably entail Bond's like numbers for the rest of the season. But as long as he keeps up his career average pace he should be of good value for the Braves. That is, unless we have to keep playing the Nationals. Because we just can't seem to beat them and I have no idea why.