When Sam Mendes directed American Beauty (his first film), the first week of rushes were apparently abominable. There was talking of putting the film on hold, firing Mendes and bringing in another director, but instead Spielberg (one of the execs in charge) told Mendes not to worry about it, wrote off the first week and told him to start again.

12 months later, and American Beauty won Best Picture at the Oscars.

That's my favourite positive interfering exec story.