I think there's a cool possibility here for the organic, more fan-driven franchises. I also think it's unlikely. Try to think of a strong and stable professional minor league in America. The ABA and CBA did basketball for quite a while until the NBA alternatively bought one league and stepped in and developed its own minor league. American football has failed spectacularly in developing a sub-NFL professional league. Even the AFL has a foot in the grave. I can't comment confidently on soccer or hockey, but I think both have semi-affiliated status.
Were the cull to happen and the new hometown teams organize (which seems tough given the new operations expenses), the MLB would see these leagues as competition, and I would imagine treat them predominately as a threat. If they did want these teams to thrive, sending them out into the wilderness is sure a strange expression of their support.
In the end, I get the whole MLB effort. But make no bones about it, this is corporate business decision and not one geared toward baseball populism (or evening the playing field or any other BS they pitch). Given the financial health of ownership, it seems unnecessary and frankly cruel, but as Reds fans know well enough, the packaging of professional baseball is myth and sentiment but the contents are about the bottom line.