I can't say if it's good, bad, or ugly. I'm not privy to what actually happened.
But I do know this... The SecNav serves at the pleasure of the SecWar and CinC. So, they don't even need a reason to fire him.
I also know that skipping the Chain of Command is a HUGE no-no.... in ANY military or federal government context. If you violate that, you're in big trouble. You JUST don't do it. Ever.