There's a fine point here they didn't mention. In the "law" (if anti-constitutional police-state diarrhea can be called that) it says that to be considered a foreign agent, a non-commercial organization has to act towards changing the state politics of Russia. So when the Committee Against Torture was considered a "foreign agent", the courts have admitted that torture is the official state policy of Russia.
The judge's excuse was that although fighting against torture is an improvement of the state policy, not a worsening, it's still a change of that policy, and all changes are verboten, even changes for the better! This would be so comical if it wasn't so sad.
Basically, Tupin is so butt-mad at the US that he's stomping his little legs in an attempt to hurt anyone who has at least a semblance of a relation to anything from the West, even if it's absolutely harmless people like the emigrant oligarch Zimin who was funding physics and math education back in Russia.