Its probably not as rampant as it is made out to be. For one, Muslims prefer to live closer to the mosques anyways, thats one of the major reasons you see them living in pockets, they other reason I guess is thet probably feel safer in "Muslim" majority areas, given the history of communal riots in India. Both Hindus and Muslims need to have confidence in the law and security of the country, but again this will take time.
Having said that, I remember The Hindu ran a story about about Muslim Kids discriminated in admission to the top private schools in New Delhi(based primarily on hearsay). At the same time after some digging I found out that the Muslim organization run Hamdard Public School openly gives 5 extra points to kids for being Muslim putting kids from other religion at a disadvantage. Now that is blatant discrimination! Yet there was no mention of that in their article.
I understand what the Hindu is doing is for a good cause, and we should all strive for a true secular society, but presenting half baked stories and hiding facts in my opinion undermines their efforts and makes one question their intention.