...interesting, as a German I'd find it more difficult to support Amnesty if they did defend the 'historian' (you don't just get to call yourself that). Amnesty does not support hate speech or calls for violence, and I'm totally okay with that.
Now consider this: the German constitution was commissioned in 1948 by the Allied Powers, there was much experience in the Commission that developed it with constitutions of democratic nations, and the Nazi experience was fresh in everyone's mind. I think the fact that Germany does not have "freedom of speech" written in its constitution wants to tell you something.
TL;DR: Germany does not recognize freedom of speech. Germans consider this to be a Good Thing.
Which actually has little to do with prisoner of conscience status by itself. It's true enough that a prisoner of conscience has her freedom of speech violated in most cases. It doesn't follow that everyone whose freedom of speech is violated is a prisoner of conscience.