Mohsen Mahdawi, an organizer of the pro-Palestinian movement at Columbia University, was freed from federal custody on Wednesday after immigration officials sought to rescind his green card.

In ruling to release Mr. Mahdawi, a federal judge, Geoffrey W. Crawford, found on Wednesday that he did not pose a danger to the public and that he was not a flight risk. The judge referenced cases from the 1950s and the specter of McCarthyism, saying this was “not our proudest moment.”

Mr. Mahdawi’s release is a defeat for the Trump administration in its widening crackdown against student protesters, although other students remain in detention as part of the government’s campaign. The secretary of state, Marco Rubio, has argued that immigration authorities have the right to eject even legal residents from the country for protest activities that the government says harm America’s foreign policy interests.

Mr. Mahdawi had been in custody since April 14, when immigration officials detained him at an appointment in Vermont that he thought was a step toward becoming a U.S. citizen. Judge Crawford ordered that Mr. Mahdawi be released from the detention facility where he had been held in the state.

As he walked out of a courthouse in Burlington, Vt., he raised his hands in the peace sign and approached a pack of television news cameras that awaited him.

“They arrested me. What’s the reason? Because I raised my voice, and I said no to war, yes to peace,” Mr. Mahdawi said. “Because I said, ‘Enough is enough. Killing more than 50,000 Palestinians is more than enough.’ ”