This article from The New Republic is a very thoughtful essay on the question of Kashmiri independence.

And Kashmiri independence wouldn't only dissolve India territorially; it would dissolve it ideologically as well. Indian secularism--Nehru and Gandhi's founding vision of a state that doesn't favor any religious group over another--is one of the great achievements of the twentieth century. It has made India more stable, and more tolerant, than its religiously conceived neighbor Pakistan. India has had Muslim presidents, Muslim Supreme Court justices, and Muslim captains of the national cricket team. By one estimate, more Muslims emigrate from Pakistan each year to India than the other way around. But to admit that Kashmir, as a Muslim-majority state, cannot remain within India would expose secularism as a lie and imperil the claim to equality of the more than 130 million Muslims living in the rest of the country--a Muslim population that today ranks among the freest in the world.