It's not just Germany, it's multiple other countries that don't allow references to Nazis unless it's for historical or artistic puposes, it's not about "hurting their feelings". These shows are made to be air world wide in case you forgot. They're not ignoring it since they still have it in their history books and films.
As for the aliens thing, you know that's not the first time the media have given Nazis "Sci-Fi" or an occult handle in shows, right?
And having heroes in these stories already makes it clear it isn't an accurate showing of history, so it's all moot anyway.
And again, you guys did notice that Red Skull is wearing an SS uniform, right? Seriously, did you actually watch the episode?
Also, your confederate analogy doesn't work, since HYDRA always had ties to nazis in the comics anyway and they are not replacing them. If anything, it's proably the same situation as in the movie. Besides, one of the earlier episdoes mentioned HYDRA was around for 60 years.