WASHINGTON — A Texas-born man suspected of being an operative for Al Qaeda stood before a federal judge in Brooklyn this month. Two years earlier, his government debated whether he should be killed by a drone strike in Pakistan.

The denouement in the hunt for the man, Mohanad Mahmoud Al Farekh, who was arrested last year in Pakistan based on intelligence provided by the United States, came after a yearslong debate inside the government about whether to kill an American citizen overseas without trial — an extraordinary step taken only once before, when the Central Intelligence Agency killed the radical cleric Anwar al-Awlaki in Yemen in 2011.

Mr. Farekh’s court appearance also came as the Obama administration was struggling to fashion new guidelines for targeted killings. The decision to use an allied intelligence service to arrest Mr. Farekh has bolstered a case made by some that capturing — rather than killing — militant suspects, even in some of the world’s most remote places, is more feasible than the orders for hundreds of drone strikes might indicate.

“This is an example that capturing can be done,” said Micah Zenko, a scholar at the Council on Foreign Relations who studies counterterrorism strikes.