Well I for one am not angry about this, and it's not like buying this Doom 3 release was ever on my mind to begin with (didn't like any of the FPS that came after Quake 1). And I never like Wolf3D either, it just didn't impress me at the time of its heyday, so for me the secret DOOM II levels were always pretty lame. But some of the textures were cool, like the banners, eagles and stuff that looked nice on some castle-themed PWADs. Even those blue wall textures were used to good effect in some maps. But they didn't have to be nazi-related, any cool designs would have done the trick. And that's the thing about nazis, they knew how to make cool designs, even if what they represented was bad. In fact, the cross itself is an ancient symbol that the nazis borrowed and modified slightly. But used in the context with adolf-looking portraits and german-speaking soldiers it definitely invokes the idea of nazi regime.
Modifiying the symbols, portraits and enemies slightly appears to remove some of the "sting" of nazi for those who want to bury such things, even though as Sodaholic pointed out burying things doesn't make them go away. But the truth is it's not even buried deep, it's a pretense in every way, shape and form. Everyone who reads about and plays this game is going to realize what those symbols actually represent, as it's no big secret the original game had nazi stuff in it, and the people who haven't heard of DOOM (all five of 'em) will read about it in game reviews and through word of mouth, especially those that start playing online. Ultimately it accomplishes nothing, because people will still think about nazis in the end.
At some point you have to wonder though how far all this censorship goes. Does germany also ban books, games and other mdia that merely mention nazis, even if no symbology is involved? And what about history books, or related stuff like WWII historical wargames (Squad Leader, Panzer Leader, etc.) It seems like it would get silly after a while, all this pretense and wink-wink-nudge-nudge erasing of serial numbers.