I don't mean to get political or assume anyone else's motivations here, but I think this conversation is getting lost in the weeds in broader ideas about what fair wages even are and what employers are obligated to pay. I think that people get so used to arguing that the government shouldn't impose a higher minimum wage that they're primed for the same arguments in a conversation about whether a specific business should pay their employees more.
Regardless of how you feel about regulating wages, it's still good to take care of people who you rely on to keep your business running. It's still good, if you can afford to, to pay your employees more than you're required to pay them. Generosity is good.
Playing baseball at a professional level takes a lot of very specialized skill and talent, and other industries that require similar levels of skill tend to pay their workers a lot more (because players will still line up and make sacrifices to chase their dreams). I don't think it's necessary to split hairs over whether or not minor league players can scrape by if they're frugal enough. Baseball organizations can afford to pay minor-league players a comfortable living, and it would be morally good if they did, even if it shouldn't be mandatory for them to do so, and even if it doesn't provide a proven competitive advantage. A business that is generous with its employees is better than one that is unnecessarily stingy.