As of this moment, Donaghy is all of it. No one else is "in on it." The only allegation that anyone else is involved comes from him. He was the only one we know of who was a compulsive gambler, he's the only one we know of who was way in debt, he's the only one we know of who had contact with the mob, and he's the only one we know of who bet on those games.
No, the NBA seems to have no qualms about changing a rule to suit their needs, so there's simply no need or sense in trying to do it under the table, because they will change a rule to try to manipulate the game during the offseason with very little regard for the consequences. When you have access to a legal weapon like that, there's simply no reason to bother trying to sneak anything else in.
Besides, if they were the type of league that were willing to do that, then they could have gone easy on Amare and Diaw. Public opinion would have forgiven them for violating the rules to benefit Phoenix.