My feeling is that the F-35 is "too big to fail". They needed to blame the pilot, and certainly didn't need anyone familiar with the defects of the plane in a prominent command or as a general.
So they fire the guy, and promote someone else that can be relied on to say that the F-35 has no more defects than any other plane had at this point in the program, and we can trust the US military industrial complex to deliver the F-47 in a similar fashion.
At the same time, you send a message: eject when your plane is misbehaving and you'll end your career. Sure, there's a risk that someone won't eject when they should, but there's also a chance that you'll be able to cover up another malfunction when the pilot nurses the plane back to base.
Did Pizzo say anything disparaging about the F-35? I doubt it. But when you've got billions of dollars of revenue/potential embarrassment on the line, you don't take chances.