I think that Hoover would have helped Woltz in this situation. Obviously, the FBI were already watching Vito, because they had people checking license plates at his daughter's wedding. And even though Hoover had a blind spot for "organized crime" that doesn't mean he would ignore a specific act of strongarm if it was brought to his attention by a friend. There's not much use for power if you can't reward your friends with it.

Woltz would probably have been killed in the long run, but I think he would have gotten the movie made. He would have been a hard target with detectives surrounding him, and Vito would have been restricted in movement by the FBI, and then finally by the war. I think Woltz would have gotten by with his defiance at least until the war was over.