The evil here is not this theory, but the fact that the Nazis had created an "empty" region by transporting out all the Poles, Jews and others. From what I can tell this man had nothing to do with implementing the Nazi "lebensraum" concept.
After the war, more than a few Nazis used the same argument you are using now. More to the point, in spite of Christaller’s alleged ambivalence on Nazis and Jews, he is still at the heart of the holocaust. More than likely he would have known about the ghettoes, concentration camps and death camps, and perhaps even assigned other planners to be in charge of where they were to go, etc. As a kid, he used to draw up maps on his own and fill in the empty space with his own utopian ideals on how the world should look.