Perhaps what we discuss here, is a historical problem. When Vito came to New York, he realized, that the government, the police, etc. couldn't handle the violence. Just the opposite - they were corrupt. In fact, the situation in Little Italy was not much different than in Sicily: You had to fight in order to survive. And Vito discovered he was a good fighter.
So becoming a Don, Vito reinforced the status quo of political corruption and violence which he had despised when he came to the US.
He did well in pacifying the gang wars.
But he despised democracy, and he did what he could in undermining it.
"My father's no different than any other powerful man, any man who's responsible for other people. Like a senator or a president. "
Chaplin's Monsieur Verdoux asks the same question in the end of that film(1947).
But Michael continues: "My father's way of doing things is over, it's finished. Even he knows that. In five years, the Corleone Family is going to be completely legitimate."
(At that time, Michael probably believed it, he hadn't got greedy, addicted to power, control and violence.)
But my point is: If Vito knew that his way of doing things was over, he realized that a new era of democracy was dawning. And chances were good, that you could make a normal business without getting involved in illegitimate activities.
The end justifies the means
No. The means are part of the moral judgment. To use your example: Truman knew that the Japanese were willing to surrender. He should have known that they wouldn't accept the Potsdam ultimatum the way it was written. He didn't even tell the Japanese what they had to fear.
Considering the means to our ends, is part of what we call wisdom.
