No, my little acerbic llama, there is no flaw in the argument.
The point about the Oppenheimer story is that he turned out to be an accomplished physicist of Nobel caliber who contributed greatly to the field. Instead, he could have been a jailbird and later a petty criminal, or maybe a major criminal. Which was better for society?
The morality, or lack thereof, surrounding the first atomic bomb is irrelevant. It wasn't his place to make policy, and he didn't make it. You may as well blame Einstein, too. From the perspective of the day, he was one of the nation's leading physicists summoned to play a role in a national mission of great strategic importance.
The bottom line here is simple. If a young person commits an offense, especially a young person working towards a career, are we better off with a knee-jerk reaction that destroys his future, or are we better off carefully weighing the prospects for rehabilitation? Which version of those possible outcomes would you rather meet on a dark deserted street some day -- the college graduate with a career, or the ex-convict who's lost all hope?--
"Everyone is entitled to their own opinion, but not their own facts."
Daniel Patrick Moynihan