This is exactly what ended up happening. After I very vocally questioned his decision, he posed the question to the entire league asking everyone how they think the "problem" (that only he created) should be solved. The vast majority of people said that the waivers should stand. So, he put all the waivers back to how they initially processed but put his foot down on the FCFS transactions since he claims we've never had them in the past (which I believe to be true).
I'm glad he came to his senses, but I still have a bad feeling about it in general. I just really don't understand how a commish can think making decisions like that without even consulting the league first is a wise course of action.