As Ant said: It was filmed specifically for the ending of GFII, it was never conceived for GF.
One other point: notice that when Tom says to Michael, "Your father and I have discussed your future many times..." Michael gives him the first of those chilling, deadly "Michael Corleone" stares that became so familiar to us in his later life. He says, "You discussed my future with my father..." Reminds me of the scene in GF where he says to Moe Green: "You straightened out my brother?"