It's okay to show the struggles of a common soldier but I personally think that the player should be made to feel uncomfortable to some degree when taking the reins of a murderous and criminal regime.
I would say that the games about war in general should make player feel uncomfortable, like Red Orchestra 2 or World at War. But games are made for a general public after all and you need a good writing team for that. Since CoH2 tried it, but fall flat on his ass in the proccess because the whole idea of struggle look liked it was just a bias towards Soviets.
If a person sees how things are going, he deserts. It's simple if a person does not want to participate in crimes. But let's be honest, the Germans did not like to disperse, at first the ideology was strong and many German veterans after the war believed that everything was right or they were afraid that they would be tortured after being taken prisoner / deserted. Obviously because these soldiers saw what was happening around and were afraid of retribution.
Its simple on paper, considering all the propaganda, the lies and the fact that your family\relatives can face repercussions at home.
Plus if your army is somewhat winning, why would you even desert. It takes a lot of self courage to do so, you cant expect it from soldiers. Not to mention that germans were afraid of soviets thats true, since they have no problem surrendering to the Americans and British, but with the soviets it was war untill the last bullet.
Its really comlicated topic. My point is, we shoudnt judge anyone on a personnel level if we dont know if the person is guilty or not, or we will end up being the same nazis blaming and killing people just because they are part of something we dont like.
Here is dialoge between Soviet spy and German general from an old Russian movie, it sums it up pretty good