It has to be said: Jerry Manuel wouldn't have needed to juggle the Mets' everyday lineup had his general manager provided him with a right-handed bat in the outfield, at second base or even behind the plate during the off-season.
Omar Minaya chose not to do that and instead left it to Manuel to fashion a lineup that wouldn't be completely exposed by left-handed starters and lefty specialists in late innings. The problem would've ideally been resolved by simply adding another right-handed position player; once that wasn't going to happen, it was up to the manager to resolve the problem.
Had Manuel chosen to abide by conventional wisdom (as his predecessors Art Howe and Willie Randolph were more likely to have done), the batting order would've had Luis Castillo second and some combination of Carlos Delgado, Ryan Church, Daniel Murphy and Brian Schneider batting fifth through eighth. Randolph especially was fond of letting young players work their way up through the lineup (see David Wright's usage in 2005) and therefore would've been extremely unlikely to bat Murphy second.
Fastballs are generally considered the best pitch for hitters to drive, because they are not as reliant on break or movement as any other pitch to be successful. Whoever bats second in the Mets' lineup will see a lot of fastballs, with a dangerous base-stealer like Jose Reyes in front and an elite hitter like David Wright on deck.
In my opinion, rookie players still adjusting to big-league breaking balls will generally benefit from batting second early in their career, since pitchers can't always get away with feeding them a steady number of breaking balls. Batting Murphy second affords him more fastballs, which should presumably earn him more hits and will hopefully increase his confidence. Castillo may have benefitted from this type of protection as well, but he surely did not last season. Besides, Castillo's inability to hit the ball over an outfielder's head makes him ill-suited to bat so high in the order.
I happen to believe in the concept of lineup protection, although like God I cannot prove its existence. I know that other people do not believe in it, but (like athiests) I'm not confident in the methodology they've used to draw their conclusions either.