I do not know. Because I dont live in India. I only get dualism based reports on tolerance and intolerance. Its either a large orange or green. with a prominent yet relatively small white in the middle.
The question is NOT of what is a hindu or what is a Muslim. here the question is of whether the Hindu-Muslim is going to be on the radar screens of such extremists in parties.
I do not live in India, neither am I in contact with anyone who has a strong religious affinity. So I cannot authoritatively answer the question of what this awareness of identity would lead to. I can share only share my experience and opinion, which may or may not reflect on society on any scale.
I know some of my friends/acquaintance/relatives who dislike Muslims. Some infact, despite not being extremist Hindus, hate Muslim. Even some Christian friends of mine hate Muslims. Indian Muslims to be precise cause I have seen them being friendly (with honesty) to Muslims here but hate the Muslims in India. So my experience says that any ostracization of Muslim, if it happens, would not be based on any religion identity. Or the religious identity would play just a part. Any hatred towards them has more causes than just religion. Because, as many posters in this forum (and my article) have said, Hinduism is all inclusive. It wouldn't/can't disapprove any religion because it is different. Hinduism itself is a pot-pourri of multiple schools of thought, from atheism, monotheism to polytheism. People worshipping cows to eating them. So can the Hindu identity by itself shun/persecute Islam? No, not without the support of multitude of other factors which exist on a certain scale.
Can any such exclusion of Muslims gain a wide support? No. Hindus/Indians by large are just like any other large, stable modern society, tolerant unless it directly affects them. People who do not bother about what others think or do. Think that religion teaches them love and peace. It is just a minority that actually thinks of dominance/violence. The current Indian society is more concerned about development/jobs/money than some sort of religious hegemony. To give an example, the hawkish and much publicized Hindu extremist Modi only talks about development. All the so called Hindu leaders have been put in the back and all the talks is about economy in the national party. It is the obvious stand for the people and party - a hungry stomach doesn't cares for religion.
Can a exclusion of Muslims be carried out without majority support? It is rare in the world that majority actually supports the national policy. Even in the democracy like India, it is rare for a govt to have more than 50% share of the votes. The majority is always the silence watcher, and a relatively small group carrying out the acts. I am sure as a Pakistani you are well aware of this fact.