I'll make the assumption that your son will be subject to D2 rules. As it happens, there is a new rule which became effective in Aug 2011. It only applies to D2 and not D1 or D3. From 14.2.4.1.2:
In baseball, softball and men’s and women’s lacrosse, a student-athlete may engage in outside competition during the segment of the playing season that does not conclude with the NCAA championship without using a season of competition. Prior to participating against outside competition during the nonchampionship segment, student-athletes shall be certified as eligible (e.g., amateurism, enrolled full time).
So if he was eligible (presumably he was) during the fall, and does not compete in the spring, he won't have used a season of competition.
If he were at a D1 school, his school would need to apply for (and receive) a medical hardship waiver, which would depend on a physician certifying that he had season ending injury.
In D3 baseball, participating in fall baseball doesn't cost a season of eligibility. But a player would lose a season of eligibility if he plays or even practices after the first regular season game, unless he qualifies for a hardship waiver.
