Wait minute - didn't the FAA eventually approve those things?
It seems that the real issue is that the FAA did not approve them soon enough to avoid disruptions to the launch schedules, and SpaceX launched instead of waiting for approval of support facility change and pre-launch protocols - not actual flight plans.
Unless the FAA can show that changes had to be made to eventually get approval for those modifications, the FAA statement that "safety" is their top priority seems to be inapplicable to these particular issues.
This is starting to look like an ego battle between bureaucrats and Musk.
I am sure Musk would rather pay a few hundred thousand dollars in fines and launch on schedule, so this isn't really about changing behavior at SpaceX. It seems to be more about trying to prove who is "the boss".
Or, maybe it is a ploy for the FAA to get more funding so they can be faster?
It certainly smells more like political posturing than public safety assurance.