But then it somes down to whether or not a player would want $500K to play minor league ball and wait vs making $500K to play major league ball and have every day count towards free agency. For a lot of these players, free agency is the financial payday they have worked for their entire lives.
Your plan might make more sense for the development of some players (like Swihart, as S5 pointed out), but that doesn't mean the players themselves want to go that route. The player and the organization can have conflicting goals in some cases, and that is possibly why they came up with the agreement as it stands...