I think some of these may have just been to help the writers stay more creative and not rely on simple crutches.
Space pirates being one of them, maybe it helped them to focus more on the "sci-fi" than a simple "and we're attacked by pirates" story?
Despite that, though, the trappings of that idea were still used, just disguised. "Rascals" was basically space pirates taking over the ship story, only the pirates were Ferengi. "The Vengeance Factor" also had a version of space pirates. "The Outrageous Okana" was a roguish space-pirate. And, of course, the "Gambit" two parter (I'm focusing mostly on TNG here)
At the same time, we saw disagreements with the crew often enough. Riker wasn't exactly obeying orders in "The Outcast". For one of a thousand examples (no idea why that's the first example I thought of).
Just because we hear about these rules doesn't mean they were followed. There's a bit of an exaggeration involved it seems.