However, religion is not the sole dimension that creates minorities. There is ethnicity (look towards North East. Manipuri and Assamese separatists are primarily hindus), language (look at Bangla Desh and Sri Lanka), culture (look at Sri Lanka and Bodos), territoriality and a whole host of other dimensions that will still have minorities. They will still keep asserting their identities.
In my opinion, the solution is to first flush out religious minorities, then proceed to cultural minorities, then get rid of linguistic minorities, then remove ethnic minorities and may be in the end we will be left with a perfect nation!