Yeah, I get that. Theo has a right to keep him in the minors if he wants to, just as Bryant and Boras have the right to raise hell over it. This is something that really needs to get changed by MLB though.
Unless there's something really funky in his contract, I don't think he's being paid millions yet (at least not by his employer, he probably has some nice merchandising deals). MiLB players don't usually get a whole lot.