I think with Amir the thing is that he loves to play basketball, he loves STJ and he loves his teammates. Those factors are huge. He and his family are not hurting financially, so there is really no incentive for him focus on one over the other. His arm is not going to get any weaker playing basketball, and in fact, with the minimal amount of pitching he has done compared to other prospects who focus solely on basketball will only help him down the line with a potential baseball career.
By staying at STJ he can play basketball during the school year, baseball during the summer, loose almost no money/value, and also get a free education if neither sports pan out in a professional manner.
I wouldn't anticipate Amir leaving until he has a 4 year degree and has let the entire basketball dream pan out.