The issue is fundamental. India believes that the entire basis for the formation of pakistan, the idea that muslims can not live together with other religions, is a flawed idea. For pakistan, giving up on this is not a choice - Doing so would mean balkanisation of the country. For India, accepting the flawed idea is not possible - Its own experience and the existence of India as an undivided nation shows that Muslims can, and have lived with other religions. Other issues like pakistani terror, Kashmir, the difference in structure of Indian and pakistani administration etc only aggravate the issue.
The fundamental issue is not religion.
The fundamental issue is the lack of total decolonization since British left. A fake Azadi.
They just handed over the entire colony, with their conquered territory, their administrative set up, the British built infrastructure and industries to the local elites (who dominated Congress).
What this means for the rest of the population is colonization would continue under Hindu upper castes.
This is what drove Muslims to unite and resist continued colonization under Hindu elites. Without this threat it's unthinkable that a Bengali Muslim, a Punjabi Muslim and a Pashtun Muslim would unite under one flag.
What do we have in common with Punjabi Muslims? Nothing. By jumping on the Pakistani bandwagon, we got rid of the Brahmins who owned all the land in East Bengal. 1971 was inevitable, but kicking Brahmins out in '47 was not.
India has an interest in occupying the Pakistan region, not only Kashmir. This threat, and the Kashmir issue, keeps Pakistan united. Religion is wrongly perceived as the single most powerful force that keeps them united. Pakistanis, though racially, culturally, and linguistically are a far more cohesive unit than the Indians (a continent basically), they are still a federation of nations like India. When India balkanizes and returns to it's pre-colonial state, that might in turn trigger breakdown of Pakistan into ethnic states.