It seems like you've articulated your objection to the R' Miller 'article', but not stated your opinion. Care to do so?
I believe that there are certain things hashem puts forth on this earth that just can't be understood or rationalized.
Going along the logic that the holocaust was caused by assimilation, I don't think we've learned our lesson. In as much as we've seen stories of people who's neshama re-sparked because of their treatment in the holocaust, there are plenty more who've completely abandoned judaism because of it. (IINM, in this year's kinus video featured a young man in europe who was raised christian, only to find out by his grandmother on her deathbed that she had been hiding her judaism for so many years - yes her grandson is slowly coming back to yiddishkeit, but that's not the point). With that rationale, I can understand why gedolim were allowed to be killed - many in cruel ways - for their culpability in not trying to be mekarev people - but millions of jews in the shtetl? Some who were frum, and knew no assimilated jews because they were confined to their little daled amos?
I've had the misfortune of losing my parents at a young age. My parents were good, g-d fearing people. They weren't blessed with wealth so they did their chesed the old-fashioned way, with their own two hands. They did g-d's work in many ways. There were moments of doubt where I thought that it was their sins or our sins that caused them to die so young - but I couldn't allow myself to think that way. Instead I focused on something different. The bracha of being alive. Both of my parents had long-term health issues that could have easily killed them at much younger ages. Hashem had different plans, he allowed them to live, raise and marry off most of their children before they passed. Every day was a blessing.
I think of the holocaust in a similar vane. Why did Chaim Yankel die in Auschwitz, and not his brother Moshe? Why were all of my grandparents zoche (worthu) to flee europe before the real trouble began, while many of their relatives did not? Why are my wife's grandparents among the few of their family members to survive?
I can only begin to imagine the complex calculus going on in heaven during that time. It's hashem's to know and not ours to find out, because it's far more complicated than we can imagine.