The Obama administration's decision to suspend some military aid to Egypt is a clear case of better late than never. Although an announcement was originally planned for August, its timing now is a warning to Cairo's military coup-makers that their repressive treatment of the opposition risks plunging Egypt into uncontrollable violence.

Troops again shot scores of peaceful Muslim Brotherhood protesters last weekend, and the next day unknown assailants struck a series of military and government targets in the most serious counterviolence since the coup. No one has taken responsibility for the attacks but it was predictable that General Abdul Fatah al-Sisi's refusal to relax the clampdown on the Brotherhood would provoke violence. In what other country in the world today is an elected president held for three months with no access to his family or lawyers? In what other country are demonstrators routinely shot without warning, not with birdshot or rubber bullets but live ammunition?

Egypt has not seen such brutal repression for decades. The last few years of Hosni Mubarak's rule now seem almost benevolent: in spite of tight overall control, demonstrations were more or less tolerated and the Brotherhood was allowed to run candidates for parliament as independents. Egypt's regime-influenced courts have started proceedings not just to ban the political party that the Brotherhood set up after 2011 but to outlaw the organisation and its social welfare network altogether. The Brotherhood's own record on human rights, during the year it had partial power in Egypt, was not good. It made little effort to rein in the police, whose abuses were one of the main complaints that led to the demonstrations in January 2011. Indeed, there were times when the Brotherhood was willing to encourage police thuggery against its opponents. Yet Mohamed Morsi's many failings cannot match, let alone justify, what has happened since the coup of 3 July this year.

Equally grim is the virtual absence of public criticism or peaceful protest from other sectors of Egyptian society other than the Brotherhood's supporters. The Twittersphere is still free for dissent and there have not yet been reprisals or arrests for posting anti-army comments there or on Facebook. The regime sees this as a useful safety valve. More significant is its flooding of the official press, the TV stations and the talkshows with grotesque smears of the Brotherhood and all its works, as well as of the few prominent non-Brotherhood figures who have spoken out, such as Mohamed ElBaradei. Primitive though the propaganda is, it has convinced an astonishing number of otherwise sensible Egyptians. As a result, politics have become almost completely polarised. The emotional tone of what passes for debate has never been more shrill, and the chances of eventual reconciliation look daily more flimsy.

Some Salafis have joined the Brotherhood's protests but the al-Nour party, which represented them in the last election, still wavers between support for the coup and silence. A few secular liberals mutter behind a comforting intellectual stance of "neither the Brotherhood nor the army", but unless this fence-sitting is abandoned in favour of open condemnation of today's main threat to civil liberties – which comes from the army – it is politically vacuous. The business community hunkers down and hopes for a few crumbs, even though the economy is in tatters and cannot live for ever off loans from Saudi Arabia and the United Arab Emirates. Tourism is dead and Monday's attacks near the Red Sea resorts, the first violence there for several years, will further delay its recovery.

Yet, far from contributing to stability, what General Sisi and his civilian followers are doing will only condemn Egypt to greater turmoil. As well as hitting the Red Sea area for the first time, this week's attacks also saw the first use of rocket-propelled grenades against government targets in central Cairo. If Iraq is any guide, the next stage will be terrorist violence against civilians through car bombs and suicide vests. General Sisi will probably put himself forward as a candidate for the presidency, exploiting the rise in violence to claim Egypt needs a new strongman. But what it really needs is a gradually recovering economy, social justice, a properly managed, non-abusive police force, a politically engaged citizenry, and the enabling environment of media pluralism, multi-party options and civic tolerance that are the true pillars of stability.