"For us, the Jews are an authentic religion of the book, and if they are not too entangled with Israel, they are most welcome in Iran, and it would be a tragedy for us if they left." In contrast, "the Baha'i's are not a genuine religion, and have no place in Iran."

Al-Imam Ruh'hullah al-Khomeini (radi'Allahu an'hu).

Having said that, the group responsible for persecuting the Baha'i was the 'Hojjatieh Society', which was banned five years after the Imam's return.  You'll note they weren't pardoned, nor was the cleric who led them elected prime minister, nor did the Islamic Republic name a military award after them.

As for reaction against the Baha'i for supporting the Shah, what you overlook in your 'Nazi comparison' is that the Shah murdered 1.3 million of his own people.  How many Germans did the Ashkenaziim kill (admittedly one is tempted to answer "not nearly enough", but I'm looking for a number here...)?