If my understanding is correct (a big if) then if he doesn't play at all for the rest of the season he wouldn't lose a year of competition. He would lose a year of D1 eligibility.
If a player had been redshirted I wouldn't want him "called up" at this point to play limited innings and lose a year of eligibility. A pitcher who would step in as a starter and play a significant role is another story. IMO, admittedly without knowing any details, the NLI ethically obligates him to pitch for the team this season if he could have a meaningful impact on their season.