Even without the full knowledge of the Holocaust, it was clear to anyone paying attention that Hitler was a warmonger and practiced extremely prejudicial policies towards "undesired" groups, especially the Jews, among whom Heisenberg had many professional colleagues and personal friendships. As Mark Walker puts it:

It hardly seems fair to accuse Heisenberg or anyone else of responsibility for the Holocaust before the National Socialist leadership itself decided to commit genocide. Thus Heisenberg's appeal to the SS for a political rehabilitation, his willingness to travel abroad as a goodwill ambassador for National Socialist Germany, and his participation in the wartime German "uranium project"—in other words, his decision to remain in Germany and work within the system—all happened or began before the Holocaust became inevitable. However, Heisenberg knew he was working for a ruthless, racist, and murderous state.

Moreover, Heisenberg did not stop working on nuclear fission, traveling abroad, or enjoying the political backing of patrons in the Third Reich once he learned of the rape of Europe, the deportation of Jews, the razing of the ghettos, or of the death camps. That would have meant taking a clear, courageous, and potentially dangerous stand against National Socialism, something Heisenberg did not do. However, it hardly seems fair to blame Heisenberg for the Holocaust. His conduct was consistent over the course of the Third Reich, It was Hitler who changed his mind.

To put it another way: there were many good reasons to criticize the behavior of the Nazis even without the knowledge of their genocide, and there were many of his colleagues, both inside and outside of Germany, who saw this very clearly and recognized the evil at the core of the Nazi state. Despite this Heisenberg put himself into positions of influence and support for the state, which was certainly more than was "required" to just get by. This is not because Heisenberg was known to be anti-Semitic in any strong way, but he was extremely "pro-German" and was willing to translate that into "pro-Nazi" in that context.

As knowledge of both the Nazi crimes and Heisenberg's work for them grew in the postwar, Heisenberg did, in oblique but deliberate ways, attempt to imply that he had not willing built nuclear weapons for the Germans but had in fact "dragged his feet" to prevent Hitler from getting such weapons. Such a thing is, from the documentary record, totally false — an after-the-fact story created by German scientists who felt that they were clearly being considered immoral for their wartime work. Which is just to say: it is interesting to note that Heisenberg (and several others of his contemporaries) felt it necessary to create falsehoods in the wake of the war, such was their difficulty of reconciling their once-secret actions with the light of day.

A very solid and readable discussion of the whole period and its issues is Mark Walker's Nazi Science: Myth, Truth, and the German Atomic Bomb (from which the above quote comes), which puts Heisenberg's activities into context. It is hard, unless you buy the debunked "Heisenberg's War" ("dragged feet") narrative, to not see Heisenberg's work as having extremely fraught moral problems, even without holding him responsible for the worst crimes of the Nazis.