Welcome, NotAnotherDon!
All these early script treatments are fascinating. You can understand why the films as released didn't include all this stuff: the films were way, way over budget and standard length, and FFC and Ruddy needed to rein them in.
So, I always consider questions like yours in the context of what actually appeared in the films that were released. In this case, "I've already made my plans" probably means that Michael was going ahead with his big deal with Roth despite Frankie's criticism of Roth. Remember: Frankie was Michael's subordinate, the underboss who ran the New York "olive oil business" for Michael, and Michael could impose his will on Frankie. And Frankie's last words to Michael were: "I want everyone here to know that there's not gonna be no trouble from me." So Michael had no reason to kill Frankie.