The verdict on Hosni Mubarak could not have come at a worse time. Discontent was already rumbling in Egypt before the conclusion of the trial of the former dictator. And although the aim was to draw a line under the past, clearing the air for the first presidential election since the fall of the regime 16 months ago, the ruling has, instead, only added to the sense of a hard-fought revolution slipping away.

Judge Ahmed Refaat may have made the right noises, celebrating the end of "30 years of darkness" and lauding "the sons of the nation who rose up peacefully for freedom and justice". But Mr Mubarak's crime was ruled to be one of omission – in failing to stop the violence that claimed more than 800 lives – rather than the graver offence of ordering it. Meanwhile, the former President and his two sons were acquitted of corruption charges and, worse, six lesser officials on trial for their parts in the bloodshed walked free.

Despite all the understandably outraged demonstrations that followed, the symbolic value of the trial cannot be wholly overlooked. For an Arab leader to be brought to book, by a domestic court, is a seminal moment, not only for Egypt but for the entire region. Neither is the relative leniency of a life sentence to be lamented. It would have been unseemly and inhumane to sentence to death so old and ill a man as Mr Mubarak, who attended court strapped to a hospital bed and suffered some further crisis following the verdict. But while the prosecution case may indeed have been weak, and the trial legally fair, the outcome cannot but foster suspicions that the old regime has been at best decapitated, not truly dismantled.

Such misgivings are far from new. Sporadic protests since the fall of the Mubarak regime have been put down with force. The interim military council has also failed to instigate much-needed reforms of either the judiciary or the police, and minimal effort has been made to find those responsible for last year's violence.

Even last week's watershed moment – the expiry of Mr Mubarak's three-decade state of emergency – may not be all it seems. There is little sign that detainees held under the now-defunct law will be released, and the tribunals convened to try protesters continue. On all counts, therefore, the military has crimped the high hopes of the revolution, and hints that it will play an overbearing role in defining the newly elected President's powers are further cause for concern.

It is for the presidential elections that the verdict on Mr Mubarak and his henchmen has the profoundest implications. To the disappointment of many of the young, liberal protesters who led last year's demonstrations, the run-off in two weeks' time is between two candidates who personify the divide between the old guard and the Islamists they fought to transcend.

The choice was never a comfortable one, and it is Mohamed Morsi, of the Muslim Brotherhood, who gains most now. His opponent, Ahmed Shafik, had hoped to benefit from liberals' wariness of Islamism in any form. But the offices of the former Mubarak-era Prime Minister were attacked in the aftermath of the weekend's verdict; and amid speculation that he might, as President, pardon his former boss, Mr Morsi spoke out for the protesters and vowed to retry the acquitted officials.

The prospect of an Islamist President remains a disconcerting one, for all Mr Morsi's alleged commitment to freedom of expression and women's rights. But what Egypt needs above all else is a government with sufficient credibility to deal with the country's growing economic problems and to heal the social fractures caused by 30 years of despotic misrule. With protesters returning once again to Tahrir Square, that need is greater than ever.