The leadership of Russia might be worried that the same techniques used by Western NGOs to depose the leadership of the Ukraine in 2014 will be used to depose them. The endgame might be that they remain in control of the government of Russia.
I believe (but of course cannot prove) you underestimate Putin. Real political threats get neutered (Alexei Navalny et al), tame opposition parties get induldged. The West is by no means sweetness and light in their attitude towards and dealings with Russia, but foment a revolution in Russia through the use of NGOs? Fantasyland.
