Everyone is entitled to make the movie they want as long as they are not promoting violence and distorting history. He may have chosen to depict a portion of history for whatever reason, but as long as that happened, he has a right to depict it. Maybe someone else can make a movie on Jammu massacre or something else. Maybe Pakistanis should make it.
There have been movies on Gujarat massacre including one I watched (named Parzania if I am not mistaken), which basically sums up the riots as a false flag operation by Modi. There are other movies too that depict Muslims and Sikhs as victims, though I agree that such movies may not get produced under the current regime. Anti-Sikh riot content is not discouraged as long as the perpetrators are shown as Congressis first.
I disagree with Agnihotri that the massacre of Pandits has been downplayed historically. It is a well known fact which most educated Indians know about and because of this they always have a soft corner for Kashmiri pundits whenever they meet them. In Mumbai University where I did my engineering, there was a quota for children of Kashmiri pandits, although a tiny one. For many Indians Kashmir is synonymous with massacre of Pandits, so I don't know what brushing-under-the-carpet he is referring to.
We need some good comedies and movies that promote communal harmony, not in an in-your-face way with a Khan Chacha like character of 70s, but movies about regular Indians of all communities living regular lives.