I don't think there's any question that Jonathan Papelbon should be the World Series MVP. The other plausible choice is Mike Lowell.
For a short series like this, it isn't enough to just look at stats. You need to measure when those stats took place, particularly when there is a 13-1 blowout game like game 1. Contributing after the game is out of reach isn't worth much. Contributing while the game is on the line is key.
That's what Win Probability Added measures. Fangraphs keeps track of this stuff. If you add the WPA from the games in which they appear, Papelbon leads the Red Sox, followed by Lowell. That means not only that Papelbon pitched well, and Lowell hit well, but that they did so at key times during games. As you know from other posts, a save is not an indicator of the pressure of the situation. Saves are sometimes available without much pressure.
However, Papelbon's contributions in the Series were at key times, particularly in games 2 and 4.