At first, I was a little distracted by the humor of this article before my brain really started to kick in to gear on this topic. Let me lay a concept on the masses here...
I will grant you that nearly every culture in today's society will overwhelming agree that Nazis = evil. No question, hands down... aside from the small population of Neo-Nazis still running through high schools and killing kids on Hitler's birthday (tasteless observation, but true). But the thing is, who else can developers cast as the token "bad guy" anymore? Middle Eastern people? Irish people? Religious zealots? Here is where the problem lies... it seems as though every other group other than Nazis has a support group that will sue game developers for insinuating they are ALL possible for being bad, even in a fictional setting. Take for example the movie "District 9" and the firestorm that created in Africans because of how they were portrayed in a fictional movie loosely based in their country. They were fine with housing non-hostile aliens, but to portray them as hording guns and prostituting female aliens seems to be too offensive... wtf? Movies don't stray too far away from video games in the genre of fantasy, and you can't even use a broad stereotype in either without possible stepping on someone's culture unless you do it in a way that is such a broad stereotype that you make them out to be a parody of them.
There aren't a lot of support groups for Nazis these days, regardless that history is written by the winners. I'm certainly not going to defend the Nazis (current or historical), but it is too easy to pin anything bad in a video game on them. They have an established backstory that developers don't need to develop, their obvious evil needs no definition or explanation, and they always seem to be working on some master plan to take over the world. No one ever questions whether or not to kill Nazis, they are pretty much like modern history's version of a whipping boy that takes all the abuse and no one has to feel bad about using them over and over again instead of developing something new. That's where modern society has failed us frankly... we don't have the freedom to pick on anyone, even in a fictional manner. You rarely ever see the United States cast as a villian (regardless of how the world at large views that country from time to time), or really the Chinese (outside of a World War 2 context).
Take Halo for example. Popular title that became the trademark of Microsoft... no Nazis. We had to travel to the future in a fictional set of events to create an enemy that no one could be offended by. These dumbass protesting hippie freaks that get pissed about every little damn thing in the world have made it so that you can't enjoy shooting anyone other than a Nazi, a zombie, Nazi zombies, or some weird-colored alien politically correct. So why in the hell aren't we shooting these picketing douche-muffin hippies instead of Nazis? Oh right... stupid pacifists. Even still, unless the violence takes place on a distant planet in the future or in some weird-ass time travel experiment (looking at you, Assassin's Creed!), you're going to piss off some special interest group and get a media backlash that will somehow affect the bottom line of making a profit without negative publicity. The answer? Throw in some Nazis, bad scripting (both in story and AI), slap some uniforms on everyone and call it a World War 2 shooter... works for Call of Duty.
I completely agree though that Nazis should be left out of future games. I'd really like to say that 2009 was the last time we saw any Nazis in video games, regardless of their role in the game. It is time we came together and decided what the new hate group was going to be for the next 60 years, but frankly, who else has the track record of bad deeds than the Nazis? Come on vigilante groups and religious weirdos, start pulling your weight so I have a different face and set of uniforms to aim at in FPS games!