As for the Greymane, he was innocent altogether and joins the Stormcloak ranks for protection the Empire failed to give him. Does this not constitute a direct violation of the WGC on the grounds that innocent Imperial citizens are suffering at the hands of this insidious enemy? Make no mistake, some prisoners may indeed be Talos worshippers but even if they are, this treatment seems extreme in my view. They cannot claim their prisoners are devout Talos worshippers because as we learn in the related quest, many, or at least one are there merely on suspicion of this. Why then are the Thalmor allowed to use this base for their gestapo-like interrogations and torture? The very existence of this place is why Nords are beginning to question the validity of an Empire that allows this to happen to it's citizens.
Skyrim is an Imperial province and thus subject to Imperial laws. It's a joke that the Thalmor are allowed to do as they please in Northwatch.