Long ago, adherents to the four major religions (Hinduism, Jainism, Sikhism, Islam) lived together in harmony. Then everything changed when the Brits attacked with the partition line. My grandfather told me that my great-grandparents' little rural town in India was diverse; there were roughly equal amounts of Hindus, Jains, and Muslims (but fewer Sikhs). Nobody held radical supremacist beliefs. When it was Diwali, Muslims used to celebrate alongside the Jains and Hindus. When it was Eid, Hindus and Jains used to celebrate with the Muslims. There was apparently a very convivial atmosphere in the town until 1947 when the Muslims went to Pakistan and the townspeople welcomed the new arrivals from Sindh.
Since the Muslims got their own country, Islamic fundamentalism and nationalism were ramped up to levels not seen for a long while. Heck, even Abu Akbar's Mughal Empire was more tolerant towards non-muslims than modern Pakistan. Reactionary politicians were elected in both India and Pakistan and "cold war" ensued, and bigotry rose to new levels.
I personally believe that the friendliness Indians had towards each other during Raj rule was because of the "enemy of my enemy is my friend" mentality. However, under a United India, there would be much less hate towards the "other religions" though you might see sporadic instances of anti-Hindu, anti-Muslim hate. For a United India to thrive, I believe it must have a strong and secular central government. If a United India was a confederation of sorts, it would be a total disaster IMHO as some local princely leaders would try to enact religious law which would cause violence.