My friend you have reduced a complicated narrative, called Muslims and nationalism, to a simple binary of Muslims cannot be nationalist where they are not in majority. Curiously while Secular, nationalist dyed in the wool congress wala like Jinnah turned coat and advocated for a homeland for Muslims, the organization which is considered the RSS equivalent in Islam Jamiat Ulama-i-Hind strongly opposed the partition. Its leader Maulana Madani, strictly opposed the partition as ply by the British to weaken Indian nationalism and explains his rationale thus against accusation that he has joined with the Hindus against Islam.
"You write that I have joined the Hindus and you are stunned by that. Why do you get affected by such propaganda? Muslims have been together with the Hindus since they moved to Hindustan. And I have been with them since I was born. I was born and raised here. If two people live together in the same country, same city, they will share lot of things with each other. Till the time there are Muslims in India, they will be together with the Hindus. In the bazaars, in homes, in railways, trams, in buses, lorries, in stations, colleges, post offices, jails, police stations, courts, councils, assemblies, hotels, etc. You tell me where and when we don’t meet them or are not together with them? You are a zamindar. Are not your tenants Hindus? You are a trader; don’t you buy and sell from Hindus? You are a lawyer don’t you have Hindu clients? You are in a district or municipal board; won’t you be dealing with Hindus? Who is not with the Hindus? All ten crore Muslims of India are guilty then of being with the Hindus."
Muslims, especially those in India, are not a monolithic community and don't express a political view that in any way anything peculiarly Islamic about it, unless we like dub all Muslims as adherent s of extremist Muslim organization that India has seen from time to time. The separatist movement in Kashmir, led by extremist kashmiri Muslims, has found little resonance among Muslims in rest of India. They have believed, in my opinion, that whatever led the Muslims in the valley to pickup arms against the state was driven by the socio-political-historical process isolated to that region and had nothing to with Islam or Muslims in India and the world in general. While there is no denying that the Muslim character of the majority in the valley added grist to the separatist mill, we will be ill advised to make that characteristic of the conflict, the be all and end all issue/solution for the conflict. This would amount to missing the woods for the forest and Indian state must refrain from doing so.