I don't see much wrong with what DePodesta's done. Dumping Green, letting Beltre walk and getting rid of the overrated LoDuca are all points in his favor. Eliminate LoDuca's fluke great season a few years ago and he hasn't been what the media hypes him to be.
Meanwhile, Drew is very quietly putting together a strong season despite his miserable start, and Jeff Kent is putting up numbers right in line with his career norms. Not only that, DePodesta's also figured out a way to keep Milton Bradley from getting himself suspended every other month. Choi's probably been a disappointment for him, and the Lowe signing might come back to bite him, but losing Gagne is a massive blow and Perez has been out for awhile now too.
The more DePodesta is able to piece together the team how he sees fit, the more games they'll start winning, IMO. The anomaly Beltre was last season contributed to quite a few wins that were probably unexpected and now they've fallen back down a bit from that.