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BAGHDAD — A frail, white-bearded cleric barely out of his sickbed proved to many Iraqis that he could accomplish in a few hours in Najaf what the tough-talking interim Iraqi government, backed by the full might of the American military, could not do in three weeks.

In ousting a young, rebellious cleric from one of the holiest sites in Iraq on Friday, 73-year-old Grand Ayatollah Ali al-Sistani needed nothing stronger than his influence. For those who envision a secular, democratic future for this country, that is a chilling fact. In the story of the three-week siege of Najaf, they say, is stark evidence that in the new Iraq the power of faith so far appears to trump the rule of law.

“This frightens me about the political future of our country,” said Wamidh Nadhmi, a political science professor at Baghdad University. “As a secular person, I respect the religious authorities, but I don’t want them to rule our lives.”

In a midnight peace deal brokered in the ancient warrens of the Shiite holy city, the unexpected intervention of an ayatollah allowed the U.S.-backed Iraqi government to avert a raid on the Imam Ali shrine, which would have risked alienating a large swath of the country’s population. But the government agreed to the deal with rebel cleric Moqtada Sadr at an unmistakable cost in influence and authority.

This weekend marks two months since the government came to power. Just as on its first day in office, the government’s central task remains to establish its power and demonstrate to the Iraqi public that it can bring the turmoil in the country under control. In Najaf, critics say, the government showed itself unable to do so.

Ismael Zayer, editor of Al-Sabah Al-Jedid newspaper in Baghdad, calls the settlement “a humiliation” for Prime Minister Ayad Allawi and his government.

“This expresses the weakness of the government, that Ayad Allawi couldn’t resolve this situation,” Zayer said. “He promised to solve the security situation. Now we have chaos.”

The terms of the peace agreement bear ominous similarities to the failed truces forged earlier this year in Fallujah and Najaf. As in those cases, insurgents were allowed to withdraw from the battle with their leadership and dignity intact, free to fight another day. Again, U.S. troops are required to depart the city, leaving security to Iraqi forces that the recent violence has shown are unequal to the challenge.

Fallujah has devolved into what some military officers describe as an “aircraft carrier for the Sunni insurgency” — a haven for kidnappers, foreign fighters and car bombers where the U.S. military is confined to little more than dropping bombs on suspected safe houses. The last truce agreement in Najaf left conditions ripe for the militia members’ seizure of the Imam Ali mosque only six weeks later.

`A tactical victory’

Still, one senior U.S. diplomat argued that the resolution was “a tactical victory,” noting that Sadr’s forces did leave the mosque this time. In June, they never surrendered their positions within the cities of Najaf and nearby Kufa.

“The fact is his forces were driven from positions they held for a year. . . . Najaf and Kufa were opened to government authority,” the envoy said Saturday on condition of anonymity.

Other analysts disagreed.

“The U.S. has rolled the rock up to the edge of a decisive military engagement, only to see it roll back down the mountain. It has fought to the edge of decisive action and now seems forced to pull back,” Anthony Cordesman, a fellow at the Center for Strategic and International Studies in Washington, said in an analysis Friday.

That sounded right to some in the Shiite corners of Baghdad who applauded Sadr for defying American pressure and compromising only under the persuasion of a higher religious authority.

“Moqtada Sadr has a good future,” said Ra’ad al Hamadawi, 32, an electronics salesman in Baghdad’s Khadamiya neighborhood. “I think he will end up in a political position because he showed he is a strong leader.”

From its origins in a routine firefight Aug. 5, the Najaf siege emerged as a direct challenge to the Iraqi government and Allawi in particular. Allawi, already cultivating a reputation for bare-knuckle toughness, responded with a vow to crush Sadr’s al-Mahdi Army, promising at one point to strike the militia with “an iron fist.”

A parade of Cabinet ministers regularly announced that an assault on the mosque was “hours away,” only to pull back from a raid each time.

Allawi’s government showed little ability to act independently of the unpopular American occupiers. Iraqi security forces played no significant visible role in fighting the militia in Najaf or Baghdad’s Sadr City slum, where Sadr’s rebels virtually controlled one of the capital’s most populous districts. It was up to American forces to retake territory from Sadr’s supporters, even as a settlement eluded the government and its U.S. backers.

Al-Sistani’s speedy results

On Thursday, with U.S. forces yards from the door of the shrine, al-Sistani arrived in Najaf from weeks in London for medical treatment. He vowed to find peace and entered the war-torn city center in a triumphant motorcade, drawing crowds of fervent well-wishers along the route. A truce was called to mark his arrival.

Within hours he had met with Sadr and brokered the deal.

When guns finally fell silent late Thursday, untold hundreds of Iraqis had been killed, as well as at least 11 U.S. soldiers and Marines. Sabotage drastically curtailed oil exports. American troops fought ferocious battles to regain ground block by block.

The peace deal afforded generous protections to the rebels. Militia members inside the mosque effectively received an amnesty, guaranteed by the government of the “right to participate in the political process.”

The Iraqi government demanded that Sadr commit to disarming his militia. But even those fighters inside the shrine were reluctant to heed that call, and when the appointed time came Friday morning to leave their weapons, many simply put their rifles and grenade launchers into duffel bags and went on their way.

“I don’t believe this truce is going to succeed, but we have no choice but [to] obey the order of the marja [religious authorities],” said Ali Adday Qasim, 26, a fighter in al-Mahdi Army who kept his gun. “I’m seeing American soldiers, but I cannot shoot them.”

Sadr returns to his home “free as any Iraqi to go anywhere he likes,” in the words of the Cabinet minister who announced the agreement early Friday. And he does so despite a much-publicized arrest warrant charging him with ordering the slaying of a pro-U.S. ayatollah killed shortly after U.S. forces entered Iraq.

At dawn Friday, Sadr’s rebels changed into street clothes and melted into the crowds of Iraqis who descended on the shrine for their first chance to visit in weeks. The worshipers scarcely hid their devotion. They shouted as they walked: “All Iraqis with you, Mr. Sistani!”