The offense was better in the second half, especially by acquiring Victor Martinez. They had a rough stretch against the Yankees for three games, but they scored 5.5 R/G in the 2nd half, and only 5.2 R/G in the first. Overall, the offense scored 872 runs. It wasn't that bad.
The pitching was the main concern, as it allowed a 4.70 ERA in the second half when some of the starters went on the DL.
They will miss Bay, but they will be virtually certain to be better at every position defensively (including potentially massive upgrades at three positions). They probably won't score as much runs as they did in 2009, but the defense and pitching will be much better at run prevention.
Besides, if the offense is as bad as you think it will be, they have plently of chips to make a run at a strong bat.