Most people would take with the bishop, it was my first instinct too. However, Seirawan recommends taking with the pawn (Winning Chess Openings p.205 on the Barcza Opening).
Of course I'm not one to be able to critique Seirawan, but I don't agree with his advice. It breaks sereval principles, and doesn't gain much in return. First, it doubles pawns and captures toward the outside, reducing your number of central pawns. These are generally accepted strategic guidelines. Second, it blocks your bishop, so in order to make your fianchetto useful again, you'll have to move the pawn to f4.
There are a few gains I can see, but none of them seem worthwhile. It does create an open file. But most people would prefer having two central pawns to the open file. It also keeps the knight off of e4. But this can be accomplished in other ways, and it alone doesn't seem to outweigh all of the strategic guidelines that are broken.
"3.Bg2 Bg4 One of the goals behind Black's strategy is to capture White's f3-Knight and follow up with ...e7-e5 in an attempt to establish a classical pawn center.
4. O-O Bxf3 Black immediatly captures the Knight.
5.exf3 I prefer this recapture, as shown in Diagram 202 (the 2nd posted fen). After 5.Bxf3 e5, Black get's to implement his plan. With 5.exf3, Black's center quickly collapses after 5...e5? 6.Re1 Nc6 7.d4! Black isn't able to play ...e7-e5 and must content himself with simple developing moves."
I think he also gave as another reason the use of that doubled pawn as a battering ram against short-castled black king, but can't remember where...
Seriwan here is using almost the same reasoning for capturing with the e-pawn as most opening books do as why to capture with the d-pawn instead of the b-pawn in the Spanish Exchange.