It wasn't just Muslims in the 30s who called for two separate states. Many Hindus did too. It's true, the most prominent Hindu in the struggle (Gandhi) wanted a single state and tried to (in theory, at least) accommodate the large Muslim minority. For those efforts he was assassinated by a religious extremist.
Of course, you hear religious extremist and you might assume it was some Muslim who thought Gandhi was too effective a voice for unity. To the contrary, it was a Hindu nationalist who thought Gandhi was a sellout to the Muslims.
This strain of Hindu nationalism that endorses the use of violence has appeared again and again. As recently as 2002 a riot occurred in which a Hindu mob murdered around a thousand Muslims.
All this isn't to say the Muslims on the subcontinent are all paragons of virtue and liberalism. They aren't. But the story the author tells is just a pleasant story, meant to appeal to the baser instincts of Wall Street Journal readers. Maybe more than that, it's a story meant to appeal to India's own self conception, where it's as pure as snow and it's those dastardly Pakistanis who've made everything terrible.