Your Professor was very likely referring to the Thirty Years' War. It was indeed ludicrously destructive, and was absolutely brutal on civilian populations.

This was in 1618-1648, so it wasn't exactly part of the Reformation proper, but a direct consequence of the Reformation. This page gathers a number of secondary sources for figures on the death toll. As it states there, modern estimates of the death toll range between 2 million and 11.5 million people, with a median of 7.5 million.

The median figure is certainly higher than any estimate of the number of German civilian casualties in WWII, which ranges between about 1.5 million and 3 million. However, total deaths in WWII including the military is a much higher figure: ca. 6.9 to 7.4 million.

The figures for the Thirty Years' War really relate to the difference between 1618 population and 1648 population, and there are more reasons for the change in population than just the war - lower birth-rate is likely to be responsible for part of that difference. And the Thirty Years War lasted five times as long as WWII. But it was still devastating. Those death toll estimates represent ca. 20-40% of the entire population.

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(Edit - realized I was citing military deaths as though they were civilian deaths; now corrected)

Edit 2 - taking loss of life in the Thirty Years War as 30%, that would correspond to an average rate of loss of life of 7.6% per 6 2/3 years (the length of WWII for Germany; and by the way, that % is a geometric rate, not linear). That's higher than the death rate of German civilians in WWII, but lower than for the entire population including military deaths. Of course the death rates in some other countries were higher still, especially Poland and the USSR.