During the second world war, we did not pretend that there were good Nazis who we allowed to immigrate here, and bad Nazis who we fought against.
You are confusing ethnic origin with ideology. Nazism and Islam are ideologies, evil ones. Germans, Arabs, etc. are ethnic groups.
And there were not tens of thousands of 25 year old German men roaming the USA on phony "student visas" planning their next acts of terrorism.
If there had been, they would have been interned or deported, and rightly so.