Defiant to a man, fighters swagger out of Church of the Nativity Â

They came out one by one, defiant young Palestinian men for whom Israel's army was prepared to lay siege to one of Christianity's holiest sites to secure their exile.

Some were jaunty – almost swaggering – as they emerged into the morning light from the Church of the Nativity in Bethlehem where they had spent 39 days, surrounded by Israeli forces. One dropped to the ground, kissing the flagstones of Manger Square, a farewell to his home soil. Another was carried on a stretcher by Israeli soldiers because he had a bullet wound in his foot.

Israel began pulling back its forces inside Bethlehem last night after the siege of the ancient basilica finally sputtered to an end, delivering victory to European, CIA, Israeli and Palestinian negotiators after several deals broke down.

Thirteen Palestinian militants – 10 Fatah and three Hamas – accused by Israel of a range of violent attacks on civilians were flown by RAF plane to Cyprus, where they were put in Larnaca's beachside Flamingo Hotel under the guard of armed Cypriot police. They are expected to remain for several days. EU officials say they will then be sent to Italy, Spain, Austria, Greece, Ireland, Luxembourg and possibly Canada.

Twenty-six others were dispatched under US escort to a new life in the Gaza Strip – still braced yesterday for an Israeli retaliatory attack after Tuesday's suicide bombing – where they received a raucous welcome from crowds. The rest of the 123 inside the church were allowed to go free after Israeli identity checks, apart from 10 foreign peace activists who held up the end of the siege for several hours, refusing to come out with the others because they objected to being handed over to the Israeli authorities. They say Bethlehem is outside Israel's jurisdiction.

The Palestinians left behind much squalor but no obvious evidence to substantiate allegations that they had vandalised the church. The basilica was littered with rubbish and was fetid with old food and bedding. Blankets and mats lay strewn on the flagstones amid the ruddy-coloured columns that run up the nave. Rice, lentils, cooking gas canisters, medicines and unwashed pots and pans were left.

The wooden altar of an Armenian chapel inside the church had been used as a food table. Someone had used the foot of the altar as a bed.

The strong stench of urine uncoiled from an alcove at the entrance, the small so-called Door of Humility, out of which the Palestinians emerged yesterday. The underground grotto, where Christ is supposed to have lain in the manger, was pristine. Some of the Palestinians had initially slept there, until priests had asked them to move out so that they could hold their daily services.

Archbishop Aristarchos, of the Greek Orthodox Patriarchate, said: "I hope that this will not happen again. It shouldn't happen. The church should always be a place of prayer, not of hostilities."

In the adjoining Franciscan compound, there was more damage. A room has been burnt out by a fire. A statue of the Virgin Mary has had its neck broken by gunfire. A lemon tree in one of the cloisters has been stripped to its branches – its leaves eaten.

Looking exhausted, Father Nicholas, a Franciscan monk from Mexico, described how he and several dozen of his fellow clergymen were caught in the middle of a conflict not of their making. "We were caught between two fires. In the basilica, we had the Palestinians and outside, the Israelis. As a Franciscan, I felt I should remain."

He said he and his fellow priests initially gave the Palestinians bread, tea, sugar and pasta. When it ran out, the men broke into the adjoining Franciscan kitchen because they were hungry, he said.

There were some reports of abuses. At one point, some Palestinians took away some Greek Orthodox candelabras, icons and pictures – "anything that seemed to them to be like gold", he said. But he said they later gave assurances that they had given them back. The Israel Defence Forces said the Palestinians left booby traps, "some of which were dealt with" by Americans, who took charge of their guns – although US sources denied this. They also appeared to have left behind a bag of grenades.

For more than a month, the rivalries and feuds that have plagued the Holy Land fused dangerously in the siege of the church, stirring many of the undercurrents below the surface of the politically volcanic landscape between the western border of Jordan and the Mediterranean. It touched on the long, aching tension between Israel and Christianity – particularly the Vatican – rooted in centuries of persecution of the Jews, and the Holocaust.

It exposed the fault lines between the Palestinian Muslim majority and Christian minority. Many of Bethlehem's Christians resented their homes, shrines and – after five weeks confined to their houses by a curfew – their livelihoods, being dragged into the conflict by Muslim gunmen. They particularly resent the local Abayet clan – four of the 13 men deported yesterday. These included Ibrahim Abayet, 29, the head of the local al-Aqsa Martyrs Brigades. His family paints him as a man radicalised by Israeli violence. His mother, Fatme, said he sold £2,700 in gold – set aside for his fiancée's wedding jewellery – to buy an Israeli M-16 rifle after two of his cousins were assassinated.

The siege became a measure, too, of the terrible decline the war has brought. Seven Palestinians were shot dead by Israeli snipers, including the basilica's bell-ringer. An Armenian deacon was also severely wounded.

There were several fires in the Franciscan compound – caused by Israeli forces trying to break in, said the monks – and gunfights close to the basilica walls. The siege began on Tuesday, 2 April. Priests inside the basilica were singing vespers when the Palestinians began to stream in, taking refuge from the Israeli army outside. The men, some armed, announced their arrival by shooting off the lock of a door linking the adjacent Franciscan monastery to the basilica.

The crowd who gathered inside the church could hardly have been more exotic. There were the permanent residents, several dozen friars and monks, most of them Franciscans but also clerics from the Greek Orthodox and Armenian churches with whom the Franciscans act as custodians of the basilica. There were a few nuns, who tended to the wounded. There were Palestinian civilians, including the governor of Bethlehem and a few teenagers.

The siege is sure now to be described as "unprecedented", one of history's nastier one-offs. Wrong. Mutual violation, disrespect and denial of one another's shrines has long been part of this conflict – whether it be the razing of synagogues by the Jordanian army in 1948, the mowing down of young Palestinians on the Haram al-Sharif/Temple Mount by Israeli forces in 1990, or the murder of Arabs at prayer by a Jewish settler in a Hebron in 1994. And it will happen again.