There is no answer to the question "what is a MiLB player worth."
But I would love to see something that resembles more of a true marketplace that the current system allows, given that MLB has an anti-trust exemption, and the MLB players have exclusive rights to bargain for the pay of MiLB players.
That ain't a recipe for a market.
So, I would like to see no draft, but a cap on signing bonuses for each team, based on where the team is in the draft order.
Also, no collective bargaining contract. Let each player negotiate for the terms. A big bonus might involve a six year commitment, and also get a good monthly salary. Some players (the equivalent of today's undrafted) might sign for a one year commitment, no bonus and low or no monthly pay, just to play and prove himself. Then renegotiate the next year with whatever club will give the best deal.
That is the only way to answer what a player "deserves" - and it will be different for each player.