jemaz - I normally see things that way as well but what swayed my mind here is he said top D2. That is high-level college baseball. It isn't like he would not develop as a player or experience the joys of a winning situation.
I don't understand your point about him him going back to the D2. He goes back as a senior? I assume that coach will have recruited by then and there no longer would be that option. If he chooses the SEC at this point, to me that would be his final stop for all practical purposes.
If playing pro is the goal, then itsinthegame is absoulutely right. You will not get drafted unless you play. One situation is almost a guarantee of playing and the other is far more nebulous especially since no money is involved. Of course, if he goes into the SEC and plays, his chances are even higher - no doubt. The whole issue is will he play.