As much as we all would have disliked to see Clemenza "flip," I nevertheless see it as an important part of the trilogy. FFC wants to show us that Michael is a different person from his father and show how power affects different people. No disrespect to Don Vito, but even he told Michael "I never wanted this for you." People like Clemenza, Tessio and Pentangeli represented the "old guard," people who were principals in the early history of the Corleone Family and people that Vito trusted. While people like Neri and Lampone were the "new guard," people that Michael trusted.

Clearly one of the main themes of II is Michael losing his soul, losing his family etc. Trying to show any remainder of Vito's wisdom had largely worn off and this would represent this further.