WASHINGTON — After commandos and F.B.I. agents snatched a key suspect in the 2012 attack on an American diplomatic compound in Libya, some Republican lawmakers urged the Obama administration to take him to Guantánamo Bay, Cuba, for a military trial, sounding what has become a common refrain — that a civilian trial for a terrorist is, among other things, too dangerous.

But on Monday, the defendant, Ahmed Abu Khattala, was ushered into a federal courthouse here, pleading not guilty to new charges that make him eligible for the death penalty. And for all the talk of security concerns, he appeared — as he had before — in open court, not behind the bulletproof glass reserved for particularly dangerous defendants. The hearing itself was routine, which is what made it so remarkable.

Five years ago, the debate over whether terrorists should be prosecuted in criminal courts was so contentious that it made its chief advocate, Attorney General Eric H. Holder Jr., a political liability. Republicans argued that F.B.I. interrogation was not suited to wartime intelligence-gathering. By extension, civilian courtrooms were no place for terrorists, who did not deserve the same rights as common criminals.

But as Mr. Holder prepares to leave office, his success in reversing the Bush administration’s emphasis on trying terrorism suspects in secret prisons or at offshore military tribunals may be one of his most significant achievements. While he did not end the debate — each new arrest brings fresh statements of disapproval from critics — the Justice Department can now point to a string of courtroom victories that his liberal supporters, as well as many law enforcement officials, believe has reshaped the government’s approach to prosecuting terrorism.