It is amazing that when all is said and done, how they compare. Napoli has been as good at the plate. And while Gonzalez is better defensively, Napoli has been pretty decent overall and certanly hasn't been a liability.
Nap:136 G, 125 H, 78 R, 36 2B, 2 3B, 23 HR, 90 RBI, 69 BB, 182 K, .257/.355/.480/.836.
A-Gon: 152 G, 167 H, 67 R, 31 2B, 0 3B, 21 HR, 98 RBI, 45 BB, 98 K, .293/.341/.458/.799.
If you look at more stats, there are others where A-Gon has a slight over Napoli. Napoli actually should have more RBIs, because his batting average is slightly lower w/RISP and w men on base than his season average. That's why I'm hesitant to say he's been better than A-Gon at the plate.
But when you look at everything, the Sox didn't lose much going from A-Gon to Napoli at 1B.