There's definitely funny business that goes on with the officiating. It's hilarious how a long-time ref got exposed, decided to come clean and talk about the unscrupulous practices and traditions that have been in place for years, and Stern just dismissed him, claimed it was a "rogue" official and none of the others were doing anything like that

and it pretty much just got successfully swept under the rug.
I think it has less to do with some huge league-wide conspiracy and more to do with the refs themselves on a smaller level. So its not "Emperor Stern says the hometeam goes down in 6" but more "Hey guys, lets make an irresponsible and irrelevant personal bet just for fun on which official can foul a guy out in this game first" or "hey isn't this player getting on your nerves? Let's send a message to him tonight and if it costs his team the game, so be it." It's insane how the officials have almost no one regulating their behavior, keeping them in check, making sure everything stays "official", so to speak, especially for how much they're able to effect outcomes of games. I also doubt very much that Tim Donaghy was the only one that ever bet on games and got involved with the mob and all that. He's just the only one that got caught.