My take would be school B, but that choice includes reasons that I was not mature enough to think about as a senior in HS.
In addition to the playing time advantage and starting earlier in his college career, he will also have potential leadership opportunities on the team earlier on. A mentor once told me that good leadership = competence + character. The academics helps to get a leg up on the competence part of the equation; the baseball experience, and how he responds with the potential adversity of being part of a rebuilding program, will help with the character part.
If you are being realistic and thinking beyond college, I think there is something to be said for the leadership/character aspect.