As you said, the novel and the movie differ. Genco's cowardice toward Fanucci was an invention of GFII. The statement about Genco smelling a rat was strictly from the novel. What makes it convincing for me is that Tom had two strikes against him as consigliere. First, he wasn't Sicilian, second, he was a lawyer. As a non-Sicilian he didn't fully grasp the irrational (to him) Sicilian need for vengeance despite the overarching risks--which is what Carlo did. As a lawyer, Tom looked to reconcile differences and avoid trials (or shooting in Mob affairs), when what was needed was violence to combat violence. The telling phrase in the novel came after Michael agreed to kill Sol and Mac. If I recall correctly, Puzo wrote: "Hagen looked glum - the statesman forced to go to war. 'At least we know what we're going to do.'."