In short, the Nuremberg Defense is bogus.

German military law had stricter language and responsibilities than Anglo-American military law with regards to obeying criminal orders. §. 47 of the Militär-Strafgesetzbuch für das Deutsche Reich stated:

If carrying out an order in the course of duty should violate a law, only the superior who gives the order is responsible. However, the subordinate who obeys it is punishable as a participant: a.) if he goes beyond the given order or b.) when he knows that the superior's order would have the aim of leading to military or other crime or violation.

This regulation dated back to the Kaiserreich and remained in force during the Third Reich. Mass murder of civilians, mass shootings of Jews, and other atrocities were still crimes under German military law. §. 47 gave any German soldier legal cover to refuse to obey them. German Jews, while stripped of citizenship and civil rights, were technically wards of the state and could not be murdered under German law. German military authorities were aware of §. 47 and its implications for destroying racial enemies of the state, but either the Germans ignored these restrictions or crafted their own orders that declared them null. The most salient example of the latter was the Barbarossa Decree of 13 May 1941 in which OKW declared that there was “no compulsion to prosecute,” criminal offenses committed by Wehrmacht troops against enemy civilians unless such offenses directly hindered German military objectives. Other decrees like the Commissar Order sidestepped procedures in favor of more violent and immediate measures. However, despite these various edicts, the legal mechanisms of German military justice remained intact. The historian Christopher Browning has found that of the decidedly small minority of Germans who did refuse orders to commit war crimes, none suffered any punishment or court martials.

David H. Kittmann's article "Those Who Said "No!": Germans Who Refused to Execute Civilians during World War II" outlines one of the more interesting examples of how discipline could be enforced for refusal to obey: Oberleutnant Nikolaus Ernst Franz Hornig. His superior ordered him and his company to shoot nearly 800 Soviet PoWs on 1 November 1941. He refused on the grounds that he was both a Catholic and a soldier. Hornig's legal background also made him knowledgeable about §. 47 and he also made disparaging remarks about these orders and likened them to the Communist NKVD's methods. It was the latter that got him into trouble and he went on trial for a undermining Wehrkraftzersetung (fighting spirit) of the men under his command. He received a four year sentence at concentration camp.

Hornig's case was both typical and atypical. On one hand, his was one of the few refusal cases that went to a military trial. His legal training certainly prepared him for this and helped his defense. He also was sent to a camp as punishment. This was somewhat different than other cases Kittmann discovered. But even here, the official cause of Hornig's charges was not the refusal to commit a war crime (Kittmann speculates that it was because he taught his men about military law). The PoW issue was secondary in his trials and it was his likening his superior to the NKVD that earned him the ire of his superiors. His prison sentence was also remarkably lenient; he was cordoned off from other inmates at Buchenwald and treated as a special case, while retaining his rank and his pay.

So Kittmann's case is interesting because it led to actual formal disciplinary hearings. But it also shows the real and limited nature of coercion in getting Germans to obey. Even though Horning crossed a threshold leading to a court martial, but both rank and established codes of military justice provided him a buffer.

Postwar investigations have yet to find a single example of direct punishment for refusal to obey criminal orders despite numerous investigations.