On a sun-drenched autumn day in L'Aquila, Vincenzo Vittorini peered into the huge hole in the ground where his house once stood and recalled the night his wife and nine-year-old daughter were crushed to death.

Scared by the scores of tremors that had shaken L'Aquila for four months, the Vittorinis were huddled together in bed in their top-floor apartment that night, 5 April 2009. When the earthquake struck at 3.32am, all three plummeted three storeys as the building folded like paper.

Miraculously Vittorini, 49, was unscathed, never lost consciousness and was dug out at 9am by a neighbour. His family were less fortunate. "My wife and daughter did not die immediately," he said, his voice trailing off. Did he hear voices as he lay trapped? "I heard everything, unfortunately."

Like many local people, Vittorini had decided to stay at home that night, having been reassured by a meeting of Italy's leading earthquake experts five days earlier, on 31 March. Just before attending the meeting, the deputy head of Italy's civil protection agency, Bernardo De Bernardinis, promised the tremors were helping the earth release pent-up energy and called the situation "favourable".

"During a tremor the day before the meeting, everyone in L'Aquila had run for the streets, but on the night of the fifth, after the meeting, we felt the initial tremors, said 'this is good, the more the merrier', and went to bed," recalled Vittorini, a surgeon and local councillor. The following morning 308 people were dead, 1,600 were injured and L'Aquila was a patchwork of rubble following a 6.3 magnitude shock.

Last week those six scientists, plus De Bernardinis, were handed six-year sentences for manslaughter by a judge in L'Aquila, a verdict that drew a furious reaction from the world's scientific community amid claims that scientists cannot be sent to jail for their findings. Enzo Boschi, one of the convicted experts, compared himself to Galileo, who was tried by the Vatican in 1633 for claiming the Earth revolved around the Sun. Another claimed the court had wanted "an eye for an eye".

After rows over climate change, genetically modified food and most recently bovine TB and the merits of badger culls, the L'Aquila trial is just the latest scuffle between science and society that has seen scientists forced out of their laboratories and on to the frontline in political battles shaping the world's future.

As a battlefield, L'Aquila fits the bill. The cracked and crumbling palazzi that line the streets of its once busy centre are now shored up by metal brackets and abandoned, awaiting reconstruction, while weeds creep along the empty cobbled streets. Bored army patrols looking for looters stand by split-open buildings where bathroom mirrors glint in the sun and washing still hangs from balconies, greyed after three winters.

Survivors of the quake who celebrated the verdict last week were quick to stress that the convictions of the experts had been misunderstood – they were not punished for failing to predict the quake, as widely understood, but for offering unreasonable reassurances that no earthquake would come.

"We were desperate for news after leaving the house repeatedly in the wake of four months of growing tremors," said Maurizio Cora, a local lawyer, who tried in vain to dig his wife and two daughters out alive from rubble when their apartment building collapsed. "That night we took the advice of Italy's most senior experts and stayed in."

One of those experts, Franco Barberi, denied he or his colleagues had offered reassurances. "I attended the press conference after the meeting on 31 March and said earthquakes were not predictable and nothing could be excluded," he said.

The problem, he said, stemmed from the optimistic interview given by De Bernardinis before the meeting. "That interview should have been countered," he said. "The civil protection agency had a responsibility to do that and evidently did not." De Bernardinis's optimism appeared to be similar to that of his boss, Guido Bertolaso, who did not attend the meeting but arranged it. Under investigation at the time in a corruption probe, Bertolaso had his phone tapped, and investigators overheard him telling a local official he was staging the meeting as a "media event" to "quieten imbeciles" who feared a big quake. Bertolaso had already decided to take legal action against a local scientist who had forecast that a surge in the release of radon from the ground was a sure sign trouble was coming.

But Bertolaso's lawyer, Filippo Dinacci, said the sense of the conversation had been twisted. "He also criticises the official for issuing a statement saying there would be no more quakes and tells her, 'You don't even do that under torture'. That is the opposite of what he is accused of."

Cora said that, even if the scientists were not prepared to rule out a major quake, they were at fault for not speaking out after De Bernardinis claimed the tremors were releasing energy. "No one denied what he said," he recalled.

"The energy release idea was nonsense, the scientists unplugged their brains and obeyed the politicians," said Giustino Parisse, a news editor at local newspaper Il Centro, whose son, daughter and father were killed in the quake. "At that meeting I think they felt the need to calm people down."

Last Thursday, local councillors in L'Aquila gathered to listen in silence to another wiretap released by prosecutors in which Bertolaso appeared to instruct Boschi about speaking to the press after the main quake. "These wiretaps show the complete control of the state over science," Vittorini told his fellow councillors.

At the time of the quake, Bertolaso was a rising star in Italian politics, often seen at the side of Silvio Berlusconi and entrusted by the then prime minister to help solve crises including the tonnes of uncollected rubbish cluttering the streets of Naples. "Bertolaso viewed himself as Superman, just like Berlusconi, and believed there was no reality apart from the one he lived," said local journalist Barbara Bologna.

Bertolaso is now under investigation for his role, butlast week denied he had ever bullied scientists. "I never needed to impose anything on the scientists who worked with us," he wrote on his website. "He has no responsibility here," added Dinacci.

Three years on, residents who were hurriedly shifted to new homes after the quake say Italy's political class has since compounded its error by delaying the reconstruction of the historic centre of L'Aquila.

A student dormitory building where eight people died remains a gutted shell, surrounded by a metal fence draped with curling photographs of the dead and withered flowers.

The town's decision to allow bars to reopen in the deserted centre brings in crowds by night, creating a surreal rave atmosphere among the empty buildings, but by day the cordoned-off streets feel like a film set, with the odd construction worker silhouetted against the Abruzzo mountains that surround the town.

"There is nothing happening, we are two years late," said the mayor, Massimo Cialente, who blames the special commissioners sent in to handle the work. "It has been like Kabul here, and I am [Afghan president Hamid] Karzai," he said. "It was not done deliberately, it was just sheer incompetence."

As reconstruction starts in earnest next year, the seven men convicted of manslaughter will be launching their appeal against their sentences.

Parisse said that, despite losing his children on the night of 5 April, he did not want damages and he did not want revenge. "We just need to learn from this. I don't want it to happen again," he said.

Vincenzo Vittorini walked away from the hole where his house once stood. "My hope," he said, "is that no one ever builds on this spot."