Don't you think this is part of the strategy to combat the "pay minor leaguers a living wage" issue? They're basically saying that if they have to pay their minor leaguers anything approaching minimum wage they can't keep all these teams. So here... you want your pay raise... you get it, if you still have a job.
It's almost like MiLB teams and owners should have thought through this contingency when they signed up for a business model that completely relies on MLB to subsidize them enough to make a profit, but on limited-term contracts that might not be renewed.
I know this is water long under the bridge, but nearly a century ago almost all MiLB teams traded being a real team hat fights for championships and players for the supposed security of being affiliated and subsidized. I guess it's worked for a long time. But maybe not any more. And there are almost no fans left to root for independent teams who try to go it on their own and make money by playing exciting baseball.