I agree that ethical WW2 games should provide at least one campaign scenario where the consequences of Nazi ideology are painfully visible, like Allied liberation of a concentration camp or mass shootings if you play as a German. The player may feel uncomfortable for a moment, but these things tend to leave an impression and it's something that needs learning.
One of the greatest scenarios in pretty much any HoI is the Götterdämmerung - a 1944 post D-day German defense (difficult but not outright impossible like the Jan 1945 one). The satisfaction from achieveing a 14 days stalemate on the eastern front or even from consolidating the Luftwaffe in the neveredning grindfests that Allied bombing bring is a wonderful experience. And it is quite hard to achieve that. I know the HoI policies on war crimes but I believe this is where holocaust events should come into play - as events that give you net advantages with the only disadvantage being the moral implications. Harsh crackdowns on civilians to suppress partisans and improve TC a bit? Authorise slave labour to help with the U-boat production? Yes, please. There should be some dilemma and there should be a concrete advantage of doing evil things (this also goes for RPG games where, even sticking just to stats and mechanics, being evil is usually flat-out worse than being good). Otherwise you either get games that avoid the topic altogether or games that take you on a roller coster ride to show you that genocide is bad. Duh.
Secondly, the authors should have the artistic freedom to focus the narrative of the campaign in any way they like. If they want to stress the senselessness of 1945 fighting, so be it. If they want to focus it on comraderie, so be it. If they want to show relations between family members or the front and the interior, so be it. If they have any focus that does not revolve around war crimes, so be it. If the direction you seek with the German campaign is the same as all your other campaigns, except that your trucks have crosses instead of stars on them, so be it. Having nazis in your game doesn't require you to also include a proportion of nazi war crimes and the vehicle to your heroism / cowardice / sense of duty portrayal can be Mr Smith as well as Mr Schmitt.
And, Jacob, I still wonder from where you take that CoH2 is denialist clean wehrmacht rubbish. You don't play as the Germans and consquently the Germans almost never get any screen time in the campaign (haven't played the Ardennes campaign, though, so if it is something related to that one, I can't know). Is it denialist because it takes a very far fetched hard stance on the Soviets while NOT taking any stance on the Germans?