First college baseball is hard - really really hard. Most here who have not seen their kids play college ball don't really understand how hard it is.
It takes incredible passion and unending drive in the face of all kinds of disappointments that they have to work through to actually play. All you have to do is search through the website and except for a few really lucky ones, most of the old timers here who have seen their kids play college ball have stories of disappointments and them having to overcome them. Now to your son.
College baseball is not for everyone. If he does not have the drive to work through one work out disappointment, frankly he will not make it in college. My son's priorities were 1) Academics 2) Baseball 3) Nothing else as he did not have the time. If your son is not 110% committed to this then this may be the best decision he has ever made, even though it disappoints you. It has to be HIS passion, not yours. If I were you I would continue to support and help him through the short period of disappointment and see how it goes in the rest of the fall season. If HE really wants to play there is plenty of time. (mine did not sign until May 1st of his Sr year)
Just my 2 cents. Best of luck to you and your boy.