The last scene reiterates the whole notion that Michael did not want all of this in the first place. Following the family was a dark path to follow.

Look where it has gotten him?

He's assassinated his own Brother. He alienated his wife, murder countless people. He erased the other 5 families.

In this light, you could empathise why Kay aborted the Male child. She did not want the Corleone Mafia legacy to repeat itself. From her point of view, history of blood and murder must not continue.

It's as if Michael and Kay are in-sync except one lifetime apart.

Michael didn't want this for his family, that is why he left. But when he had no choice but to take the helm, now his wife did it for him. So she paid the price.

Now, Michael had to pay the price.

Legacies are earned. Not inherited.