I'm not pretending this is some magic ticket to puppy-rainbow-fairy land where retaliation never occurs, but ultimately, how much do you care about your shipmates? I had a CPO once as one of my direct reports committing major misconduct and threatening my shop with retaliation if they reported it. I could have helped crush the bastard if someone had come forward to me, but no one ever did until I'd turned over the division to someone else, after which it blew up. Sure, he eventually got found out, but still. He was a great con artist and he pulled the wool over my eyes, but all I'd have needed is one person cluing me in to that snake.
Speaking from the senior officer level, we're not all some cabal trying to sweep shit under the rug. And the IGs, as much as they're feared, aren't out to nail people to the wall who haven't legitimately done bad things. I'm sorry you've had the experience you've had, but that doesn't mean that everyone above you was some big blue wall willing to protect folks who've done wrong.
Individual A reports a unique or rare problem. Everyone knows it is reported by person A.
Nothing is done.
Person A reports the problem "anonymously" to some third party, which raises a stink about the problem.
Now everyone knows that person A reported the problem to the third party.
This is why I (almost) never blow the whistle. It's an automatic career-ending move, and any protections are make-believe at best.