In the reddened portion, you are commiting a logical fallacy in equating Pakistani with muslim. Even if an Indian wants a genocide of Pakistanis (most don't, BTW), it doesn't logically follow that he or she would then want a genocide of Indian muslims.
Indians' enemity towards Pak is mostly on the basis of geopolitical hostility, not religious. And the last statement of yours is an unsubstantiated generalization. Most of the warmongers in India have a hatred of Pakistan in their minds, not a hatred of muslims. The very idea of India as a nation state is one where all religions are equal in the eyes of the state - anybody passionately espousing the idea of the modern day Republic of India would also be wedded to that idea.