I agree with that. However, I think it is learning to overcome those primitive brain functions that leads to one becoming a better person. A person ruled by reason and logic, not emotion. Emotion is fickle. Logic and reason are not.
You do indeed need to do some research on this subject. "emotion" is NOT part of the primitive brain at all. And, while fickle it may be, it is located entirely in the frontal cortex. 
Try to envision our brain as a house. The foundation would be the first thing erected. It is what holds up the rest of the house. It is the "primitive" part of our brain. Then as we add on the upper floors, (frontal cortex), we are then including the parts of our brain that go beyond what reptiles have. We add in emotion, and higher forms of reasoning. 
To say that we should eliminate the foundation, to somehow achieve enlightenment is ridiculous. It assumes that just because we have a part of our brain that is similar to lower animals, that this part is not needed. 
We are indeed different from lizards. And so are all mammals, different from them. Just take a look at the foreheads of mammals, compared to reptiles. We have foreheads because our brains have grown out, and forward, from our primitive brains. 
Chimps have very large foreheads compared to other mammals, but when compared to the human brain, you can see how it slopes back, and is not as pronounced. They DO possess emotions, and higher forms of reasoning from other animals, just as we do, just not as developed as us.
So to sum up- Without the foundation, the house can NOT stand. To create a better house, you can add more floors, but you can NOT tear down the foundation. 
To your other point about the mistreatment and punishment inflicted on Germany after WWI, is very true. But in my mind, is only a lame excuse for WWII. They were the bullies on the block in the first war. They were smacked down and punished, just as any defeated regime would be. 
The main reason for WWII is because of the Depression that the world was going through. At times of drought, famine, economic depression, etc.  It is much easier for people to be led down the road to war. At times like these people will gladly follow leaders that proclaim Righteousness, and blame all the woes on others that are less human, and less deserving. 
Hitler with his Superior Race diatribe, was just what the people wanted to hear. They wanted to believe that they were not the ones, that were responsible for their own suffering.
They wanted to believe that they were at the top of the evolutionary ladder. Their economic situation could be fixed, if only the sub-humans could be culled, from the Species of man. 
People like Adolf Hitler are as common as con men. They are people with the combination of skills that include a.) knowing how the group mind works. And b.) the intense desire to rule over others.
The world today is standing on the edge of that same cliff that preceded WWII. We can be thrown into another Great Depression tomorrow. God help us if this happens, as there are many Con-men Hitlers waiting in the wings, to take advantage of the situation.
For this reason, I think that it is now the time to speak up, and shout down any and all, that would shit from their mouths, as Hitler did. You said it yourself that at some point it becomes too late. The secret police are just around the corner, if not already here.