a) This is not a diplomatic matter, since diplomatic reasons were not involved in Modis application for visa. Modi doesnt represent Govt. of India, but the State of Gujarat. Modi is refused a visa because of Modis (in)actions. If Modi is refused a visa, why should the PM be refused visa? The buck stops at the office of PM, but he is not responsible for phenomena such as post polarization victories this countrys statesmen make following genocides. So, wrong, the PM is not ultimately responsible for whatever happens in the country.
b) It is one thing that the US does not have clean human rights record. But that is no reason for that country to necessarily grant visas to other human rights violators. No thief would want his own stuff robbed.
If the secularists are behind this visa denial, then, good for them. A huge effort from their side, a slap on the wrist for a genocide perpetrator.