This sounds like a bad situation. TIFWIW, but if baseball is of importance, I would look elsewhere and take it as a lesson learned. Usually there is nothing to gain by forcing the issue. Yes, you could fight it and you might even cause problems for the coach and program, but in the end that won't help your son. There is probably no way he will be treated fairly in baseball at that school.
The Big 12 is a top conference, while the school in question might not have lost players to the draft, many other programs did. My guess is that someone recruited by a Big12 College should be able to find another DI program that wants and needs him.
Unfortunately this will require some quick work, but it might be well worthwhile. I'm a big believer in fate, sometimes what seems like a catastrophe turns into the most fortunate break. It's too bad this happened, I feel for you, but it ain't over till its over! Things often work out, no matter how bad it seems.
Spending your time fighting isn't likely to help, spend that time finding a good college. Use every resource possible. It will be interesting to hear how things turn out.
Best of luck