Given the long history of Clemenza and the Corleones, and the differences between Clemenza's and Frankie's personalities, I don't think that simply substituting Clemenza into the Pentangeli plotline would have made for a plausible betrayal.
I think Clemenza's presence in the film would have required a very different tack to make the betrayal plausible and tragic.
You hit the nail on the head.
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