NEW DELHI — To India’s prime minister, Narendra Modi, eliminating the autonomy of Kashmir, a disputed, predominantly Muslim territory, was an administrative move, something his ministers had presented as simply a long-overdue “reorganization.”

But to Mr. Modi’s critics, the decision was an attack at the heart of India’s secular identity and a historic blow to a democracy that celebrates itself as one of the most free and stable in the developing world.

There is little doubt that Kashmir needed fixing. It is one of the bloodiest, most stubborn flash points in South Asia, a complicated, disputed mountainous territory that several times has driven India and Pakistan to war.

Both nations wield nuclear weapons and claim parts of Kashmir. For decades, their prickliness has kept the region trapped in a low-intensity conflict, leaving it depressed, full of rundown villages and the backdrop to a quixotic battle between a few hundred young militants and tens of thousands of Indian troops.