I realize that you're not very concerned with the details of the situation here and that this is a metaphor and whatnot, but I'm a stickler for factual accuracy.
"You are General Eisenhower. It is 1945. You have just triumphantly liberated Berlin. As the remaining leaders of the old regime are tried and executed,"
General Eisenhower did not liberate Berlin; it was liberated by the Russians per inter-Allied agreement, as it was east of the Elbe River and thus fell into the Soviet zone of occupation. The Nuremberg defendants were not executed until late 1946.
"Soon, "Nazi" comes to just be a synonym for "good person". If anyone's not a member of the Nazi Party, everyone immediately becomes suspicious."
Germany was already like this in 1940. The main exception was the military (hence the July 20 plot), although even they were expected to be loyal to a much higher degree than is common nowadays.
"Good Nazis love real, physical Jews! Some Jews even choose to join the Party, inspired by their principled stand against spiritual evil."
This would never, ever, ever actually happen. Germans were already anti-Semitic before Hitler, and had been subjected to more than a decade of relentless propaganda (Der Sturmer and the like). Needless to say, no Jew would ever associate themselves in any manner whatsoever with an organization that had just killed most of the Jewish population. Nazi symbols (the swastika and the like) are still illegal in Germany, sixty-five years later, largely for this reason.
"Today, in 1945, mixed race marriage is still considered taboo by most liberal societies, including the United States."
There was definitely stigma against it, but it was legal in many states (http://en.wikipedia.org/wiki/Anti-miscegenation_laws#Anti-miscegenation_laws_repealed_until_1887); many more states than gay marriage is legal in today, actually.
"even in that universe, Germans would keep a strong cultural identity and find new symbols of their patriotism."
Germans today seem to be generally antagonistic to overt nationalism largely because of their history (Germany didn't even have a national anthem until 1952, despite the obvious difficulties that caused).