Max well, The Maharal in Netzach Yisroel is not a halachic work. In addition, how could he possibly be paskening yehareg v’al yaavor for something which is not one of the big 3. Obviously he does not mean this halachically.
In addition, the Shalosh Shevuos come from a pasuk in Shir Hashirim, and divrei torah midivrei kabalah lo yalfinan. Any halacha from nach can’t be more than drabanan, at best, even if it was halachic and not aggadic.
Finally, the fact that aggada informs our out look is fine. It means the Shalosh Shevuos are there to teach us hakaras hatov for our host countries and to be good citizens. Yet, I doubt that nice idea applied to the Nazis, yemach shemam. If there was a way to rebel and defeat them, we would have been obligated to fight them tooth and nail. It is all a matter of seichel. When people treated us well, we treat them well. But we have seen plenty of wicked and evil rulers in our history, and in those cases, haba lhargecha hashkem lhorgo applies.
Finally, after the Holocaust, where were the refugees supposed to go? Every country had kicked us out. Do you seriously think G-d is angry that these broken people took the remnants of their torn lives and decided to start over again and rebuild in Israel? It was pikuach nefesh.
I have heard from a gadol (in other circumstances) that one can make an avodah zara out of a mitzvah. It seems to apply here. Everything must be balanced with seichel. To think the RBSH would be happier if Arafat were in charge of Israel, or that Jews must now go back to Poland or Germany where we were treated so royally, is just totally insane. No religious obligation can be insane. If it is insane, it is not the will of the RBSH.