I think that was not the point of the article. Islamic fundamentalism or Hindu extremism had always been a sad reality of undivided India's national life right from the days of the early Mughals to the last days of the British and one has to be too naive to believe that a Shiv Sena hooliganism or a Sipah e sahaba sectarian violence could not have happened had partition not taken place.
What the author tries to pursue, in my opinion is an idea of an India, divided into three zones A, B and C where zone B and C comprising Sindh, Punjab, Baluchistan, KPK (in the West), Bengal, Assam (in the East) as autonomously administered provinces where the Muslim majority could enjoy their basic rights without the fear of intervention from a Hindu majoritarian rule. This imagination, if materialized could have avoided the appalling bloodbath of Hindus, Muslims and Sikhs who lived in areas as minority in those respective provinces.
Further, the Muslim working class scattered all over India, who had neither means nor resources to move to a far away alien land on such a short notice would have had ample time to move if they wished and felt their religious sentiments are being hurt by a Hindu majoritarian rule in province A. Thus, there would been little or no scope for abuse of one's individual liberty threatened by the socio-cultural or religious interests by the ruling majority. Akhlaqs could eat fearlessly whatever they wanted to or the secular bloggers and Taslima Nasrins in India could enjoy their freedom of expression, sitting in Calcutta. Thus, the uneasiness, the fear of being challenged on the grounds of one's religious beliefs or political inclinations could have been evaded.
Gen Sahib, if those are the successful realities of federalism, there had been monumental failures also. Czechoslovakia the only democratic country curved out from a chunk of Western, Eastern and central Europe came to the verge of extinction when large part of its ethnic minorities decided to cede away on slightest provocation from the west despite repeated guarantee of autonomy. A Czech experience is much more apt to compare with an Indian scenario, in my honest opinion.