I think I figured out why they changed the name. It doesn't have anything to do with PC or German laws (otherwise they would've changed the names of the axis bombers and such). It has to do with cohesion with Iron Maiden lore.
In the stage where you battle the Corrupt General the clairvoyant tells you the leaders of the 2 sides have been corrupted. In addition, the name of the stage is "Heart of Darkness", a song about the book of the same name and in the lyrics there is a line "The general's gone rouge and his methods are unsound."
It just didn't make sense to call him a Commander. My theory anyway..