...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.
The German constitution does not recognize freedom of speech; what it does recognize is freedom of political expression. There's a limit to this, though, when it is perceived to endanger public peace. Holocaust denial and suchlike has always been considered an assault on public peace. No public figure will be seen denying the holocaust or similar, the only purpose of that sort of statement can be to incite a mob. That's the background.
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.
I think that it is. There are limits to speech everywhere, whether it is the prototypical "fire in a theater" example, or making threats. It is simply another in that category.
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.
I don't claim to be an expect on Irving, but a cursory glance at Wikipedia shows that he is an active Holocaust denier that an English court found "persistently and deliberately misrepresented and manipulated historical evidence." I'm sure there is more to his story, but to say that he "certainly deserves" to be called a historian is pretty simplistic.