I listened to an interview with one of the article's authors, and she said the reason non-violent protests defeat a state willing to order violent crackdowns is

I listened to an interview with one of the article's authors, and she said the reason non-violent protests defeat a state willing to order violent crackdowns is because the soldiers performing those crackdowns are regular people. They are not the people who most benefit from an authoritarian state. So when they find themselves being told to beat up or shoot a nun sitting in the street, there's a good chance the soldier would defect.