Stop seeing from a religious angle. For a moment imagine this is a fight between white people ( moghuls/turks ) and south asians. Do you also notice how some members of India's punjabi elite feel more at home with their "pakistani friends" than with the other Indians ?
The elite of Pakistan is made up of descendants of erstwhile Moghul/Turkish rulers who form the elite in Pakistan. This elite in Pakistan hankers for the the days of the glory of moghul/turkish rule when they formed the ruling class. This Pakistani ruling class has used religion for its own end while being educated in westernised convent schools of Murree ( like our Doon and Sanawar school ). They have used the people in North -West provinces - the Pathans and they have used the lower class muslims in Pakistan to forment trouble in India. The same have now turned against this elite now - the army and the upper echelons of bureaucracy/industry. The fight is not between Hindus and Muslims but between the white race ( turks/moghuls ) and other south asians. The white race has turned Indians against other Indians using religion.
Jinnah founded Pakistan NOT for religious purposes but because he did not accept "Indian" masses ruling the country. Elite white muslims migrated to Pakistan leaving behind their converted desi brethren to their fate.