I don't see how terminating (actually it would be not renewing) the player development agreement violates any legal concept. Each MiLB owner still owns the stadium (or has a lease), and can put whatever team into it; MLB simply provides the players.
To hold otherwise would be to lock in a system regardless of new and better systems emerging.
Here, MlB isnt even taking in-house an outside profit center, just to take that profit (think Amazon). MLB believes it has a more efficient method to accomplishing its mission: MLB players. In fact, hiring the computer/stat guys costs more for each than a minor leaguer or a bunch of guys, the hardware and constant upgrades needed are expensive. This is a technologically driven change. Has nothing to do with MILB (it's not personal, its business).
MLB doesn't exist to support MILB.