Thats hardly a proof , is it ? Just a bunch of anti-hindu activists trying to defame hindus in the eyes of the world.
I don't think Freedom House is anti-Hindu. They are a very respectable fair-minded organization who monitor countries around the world in a realistic manner. They are no Amnesty/Human Rights Watch leftists. They rate India highly on their Freedom Index.
While I personally do not agree with the decision to deny a Visa to Narendra Modi, I don't think problems should be swept under the table either.
Several Indian posters here who are Hindu have also spoken against Modi.