There's a huge difference between being 26 and doing something every day of your life, and being 26 and not doing it in 3 years. I speak as someone who has been a professional athlete and trained pro athletes for a large chunk of their life.
He didn't just miss time, he missed developmental time. The time that he won't get back now because now he has to pitch in the bigs. This is bad because it really screws with the kid's development. No matter how well in shape he stayed in the military, it was not functional towards baseball, and he wasn't under the supervision of MLB pitching coaches facing live batters.
He has talent, yes, talent is only half the equation. Franchy Cordero had all the talent in the world and he laid eggs without missing any time. You need development, and you NEVER truly know how a human being is going to develop. Do people really sincerely think we should have protected Noah Song? It really just boggles my mind.