Although my focus was much more on interwar German cultural history, I do vaguely recall some speculation about Soviet intents pre-June 1941 in some of my seminars. But if you want to talk about political controversies and relatively recent history, well, there's always the Historikerstreit of 1985-1989. Now that was where political views truly and deeply affected scholarship of the Endlösung. Even 30 years later, it still is a very contentious issue, but as the WWII and immediate postwar generation dies off, I suspect there might be a more nuanced look at the Sonderweg thesis, Functionalist vs. Structuralist arguments, and perhaps people like Daniel Goldhagen won't write such ill-argued books that get NY Times attention A one-time History MA can dream, no?