The balance of power in Syria was changed forever on Wednesday. Inside a nondescript three-storey building in the heart of a secure zone in Damascus, three security chiefs were dead and a fourth mortally wounded as the Middle East's most ruthless regime was rocked to its core.

The rebel force filming nearby had just detonated a bomb inside the inner sanctum, something that was never supposed to happen in a state rooted in four decades of totalitarian rule and anchored in fear.

Panic was clear in the voices of the emergency responders, whose radio calls were intercepted by the watching rebels. Their frantic alarm, claim the rebels, showed a dimension to revolutionary Syria that did not exist even hours earlier and had never been a trait during the dynastic rule of the Assads.

Even during four embattled days before the bombing, the regime had maintained the appearance of control as a large rebel force advanced on the capital from three directions – the first time such an assault had been launched in 17 months of violence. There is no calm anywhere any more.

Now, with Syria's rigid order ever more vulnerable and its neighbours increasingly alarmed, planning for life after the regime is well under way. That Bashar al-Assad is finished is now a given; far less certain is what will be left of Syria in his wake.

The key ingredient in the regime's longevity – fear – is no longer the glue that will hold it together. As loyalist troops battled rebel forces in Damascus this weekend in an attempt to seize control of ground they had lost in the capital, more senior generals than ever had announced they had switched sides. Defections, or desertions of more junior officers and the rank and file, are widely reported across the country.

There is now a real sense among diplomats in Beirut and the exiled Free Syrian Army leadership in Turkey that a catalyst has been reached, perhaps well before anyone was ready for it.

"In many ways, they got to this point before they or anyone else has prepared for the next phase," said a western official in Beirut. "There are no credible systems in place among the Syrian National Council, or anyone in the opposition groupings, which could act as a buffer to chaos."

Wissam Tarif, a senior official from the global campaigning organisation, Avaaz, said an urgent appeal to Syrians living in exile was needed to help prevent a highly dangerous power vacuum that will likely follow the crumbling of regime authority.

"It will require highly skilled people with advanced material skills to prevent sectarian war," he said. "There is a huge task in trying to get people home. We haven't heard of any initiative or planning. There is a transition plan, but no planning for who is going to fund the transition period."

Forty years of police state has crippled any meaningful development of a civil society in Syria. The key institutions of state remain interwoven into the Baath party, which has acted as the eyes and ears of the regime, and the pillars of justice, such as the rule of law and court system, are far from independent.

When the corroded institutions of state fall along with the regime, there will be next to no checks and balances. The looting and bedlam that followed the fall of Baghdad is very likely to be repeated in Damascus, unless order can somehow be quickly secured.

Earlier in the uprising, the Syrian National Council was groomed by the west, the Gulf states and Saudi Arabia as an alternative administration that could offer a more pluralistic, representative rule and convince the country's citizens that it was ready to take power.

But relations between all potential patrons and the SNC have cooled considerably since the start of the year, with many now doubting that their leaders can assemble a credible body. The Syrian people whom they were supposed to represent are just as underwhelmed.

"They fight more than they work," one US official told the Guardian. "And they don't deliver." And, according to members and western observers alike, some senior leaders who have received money sent to fund the administration have not passed it on.

"I was at a meeting in Cairo in May," said Thaer Abboud, a member of the Alawite community who has worked against the Assad regime, at times with the SNC. "It was an important gathering in the Semiramis hotel and Robert Ford [US ambassador to Syria and now a key member of the National Security Council's Syria strategy group] was there. One delegate, a well-known SNC member, started accusing the Americans of not helping them, not doing this or that.

"Ford replied that he was the one a very large amount of money had been sent to, and where had it gone? He sat down and didn't say a word and was chased out of the room by the other people there. It was shameful.

"One thing that we have in common, all of us, is lack of trust. The SNC should be the most credible body to negotiate in the name of people. But it is not able."

As the SNC bickers and falters, Syria's Muslim Brotherhood, long a pariah body under Assad and his father Hafez, has been quietly building support. It claims to have the ear of no more than 25% of the population, after a year of low-key work, primarily through its three seats on the SNC's executive committee.

The group's slow-burn style is replicating the work of its counterpart in Egypt, which won democratic parliamentary and presidential elections held this year after the 2011 fall of the veteran dictator, Hosni Mubarak.

A prominent role in Syria for the conservative Islamic group, with links to the Sunni Arab powerhouses, is one possible outcome in the wake of the regime. "We are ready for the post-Assad era, we have plans for the economy, the courts, politics," the Brotherhood's spokesman, Muheim al-Droubi, told the wire service Agence France-Presse. However, he added: "My opinion is that in free elections the Muslim Brothers wouldn't have more than 25% of the votes."

In Syria, the Brotherhood has unfinished business with the Assads, dating back to a massacre in 1982 launched by Hafez al-Assad, which killed an estimated 20,000 people in Hama. The killings of large numbers of Sunni Muslims during this uprising, ordered by an officer class dominated by the Alawite sect, has only added to a foreboding spectre of revenge that is looming ever large as order continues to decay.

"There won't be a Tahrir Square moment in Syria," said Tarif. "Revenge is a problem. How do you manage that? You need those officers who have defected to come back and take charge. They will have to at a certain point make concessions to prevent a total collapse; a country with no leadership, fighting among groups and sects."

A long-mooted contingency plan for the regime has been to retreat to the Alawite mountains in northern Syria and carve out a homeland from there through to the heartland of the sect in the coastal cities of Latakia and nearby Tartus. Many among the mysterious, heterodox sect with loose links to Shia Islam are believed to see the violence in Syria as an existential threat, which will escalate if the regime falls. Other Alawites say they resent that their sect has been hijacked by the regime and used to solidify its rule. "We can't be separated from them as a people," said one Alawite man in Antakya. "The trust is so broken down that we will be tarnished by the regime no matter where we stand."

A potential balkanisation of Syria, which would possibly be linked to outright sectarian war, would be deeply alarming for the region. The sectarian tinderbox that is Lebanon, 21 years after its own sectarian civil war ended, could easily be reignited. Iraq, slowly recovering from a more recent civil war of its own, is by no means stable, or immune.

Turkey, which does not want to let Syria's woes give the region's Kurds a raison d'être to press their claims for statehood, would clearly feel threatened if the nation states carved out of the Arabian deserts in the wake of the Ottoman empire suddenly came tumbling down.

Shashank Joshi, research fellow from the Royal United Services Institute, said: "We should also not exclude the possibility of prolonged resistance from rump security forces, including the concentration of regime security forces within Damascus or in 'Alawite' areas in the Levantine highlands.

"It would likely result in a longer-term defeat for loyalist forces. An Alawite mini-state would be outgunned, isolated, and opposed by Turkey, but such a defeat could only come about after a deeply divisive and casualty-intensive process entailing the temporary balkanisation of Syrian territory.

"If state authority were not established within a reasonable period after collapse, the longer-term prospects for a democratic, stable Syria would shrink even further, because local militias would gain in strength, helped along by foreign powers eager to cultivate clients – a process familiar to us from Lebanon's civil war. What is clear is that the past few weeks' series of defections, assassinations, and the loosening grip of Damascus all indicate an ever-narrowing base of support, and a high probability of sudden and unpredictable collapse."

A veteran Beirut-based diplomat agreed: "The Alawite issue in the transition needs to be addressed in a very clear way. There has been nothing done by anyone, ourselves included, to give them the comfort they need. The Christians as well, for that matter."

One way to avoid the abyss is the anointing of a hardman to take over. Defected general Manaf Tlass, a former friend of the Assad family, is a potential candidate. The lessons of Iraq dictate that former regime figures cannot afford to be sidelined when a new state is built. Tlass has yet to reveal his hand, but he – and others like him, who waited many months before defecting – are increasingly being treated with suspicion.

"These people should be engaged and integrated," said Tarif. "There are other officers like him who must play a role. Order is preferable to chaos."