What would be the appropriate salary for a Minor League player?
I believe this question goes beyond federally regulated minimum wage, and goes beyond tangible profits generated directly by each minor league affiliate. A wide-scale study combining the cost of a farm system, combined with the resulting average success of a prospect at the Major League level, would probably be the only way to properly value a Minor League player. Even then, as profit margins change nearly daily at the Major League level, it'd be tough to pin down an appropriate figure.
Since most MLB have 5 or 6 affiliates they might have to ante up a bit to keep them. After all having 75 pitchers in your organization has got to be better than 30 if you only had 3 teams.
I don't think the amount of money involved would be large by MLB standards. Assume there are 100 players at A ball on down in each organization, to bump up pay by say an average of $5,000 per player is $500K per year. Hardly a bankruptcy expense.