The imprisonment on blasphemy charges of Jakarta Governor Basuki Tjahaja Purnama, better known as Ahok, has been a blow to hopes that his earlier success in public office represented the emergence of a more pluralist politics in Indonesia. There is little question that the accusation that Ahok had insulted the Koran, for which the evidence was always quite thin, contributed to his defeat in polls last month. Sadly, his defeat and imprisonment may discourage others of Ahok's ethnic and religious background from seeking public office.

Yet some journalists have gone further, arguing that Ahok's defeat and imprisonment are not just a solitary victory for the Islamists who demanded his ouster, but an indication that Indonesian Islam is increasingly intolerant, that its democracy is moving in a fundamentally illiberal direction, and that a well-funded coalition of Islamists and populists will ride the wave of these changes to victory in the next presidential election in 2019.

But there are also reasons to believe that these analysts have overstated the broader implications of the verdict, and that Indonesia will revert to form.

First, Indonesia has never been as tolerant as the clichéd praise of journalists and visiting dignitaries would suggest. Though the constitution allows for freedom of worship, this is in practice a group right rather than an individual right. The state authorises adherence to one of six religions, but citizens are not free to deviate from these six, and can be prosecuted under blasphemy laws for challenging religious authorities. Over 100 people have been charged with blasphemy since 2004. In the case of Ahok, the defendant was unusual, but the charges were not.

Indonesia's system of group rights affects how Muslim leaders and many of their followers think about politics and the role of religious minorities. Social cohesion is often placed ahead of freedom of conscience. For example, surveys conducted by Boston University's Jeremy Menchik in 2010 illustrated that even among the most tolerant Muslim groups in Indonesia, most clerics were opposed to the idea of a Christian serving as a leader of Muslim-majority areas like Jakarta. In other words, Indonesia is tolerant but not liberal.

Second, some research suggests opposition to Ahok may have had more to do with anti-Chinese sentiment than the influence of political Islam. During the Suharto era, even as Islamist organisations were suppressed, Indonesian leaders libelled the ethnic Chinese minority as a foreign business elite of questionable loyalty, curtailed their participation in public life, and stoked popular resentment to deflect criticism of their own cronyism, especially when economic growth faltered.

Under democratic rule, conditions for Chinese Indonesians improved, but indigenous elites have periodically returned to anti-Chinese rhetoric. President Jokowi's opponent in the 2014 presidential election, Prabowo Subianto, frequently used rhetoric that implied Chinese Indonesians were foreigners enriching themselves at the expense of their fellow Indonesians. And few Chinese Indonesians in the democratic era have succeeded in winning executive office. Again, Ahok was the exception, not the rule.

There is, however, a broader constituency for anti-Chinese populism than there is for political Islam, so it would be a mistake to assume that all those who marched or voted against Ahok also support the Islamist agenda. Some Islamist leaders, emboldened by Ahok's fall, say that they plan to tap into resentment against ethnic Chinese to push their agenda further. But without a target as prominent and polarising as Ahok, it will be more difficult to use anti-Chinese populism to mobilise popular resentment to the same degree.

The protests against Ahok last year that appear to have pushed the Attorney General to lodge the blasphemy case were very well-funded – and not for religious reasons. The largest protests since Indonesia's return to democracy received unprecedented financial and logistical support from an ad hoc coalition of political party bosses seeking to defeat a close ally of the president ahead of general elections in 2019 (as Jokowi himself demonstrated in 2014, the Jakarta governorship is the ideal launching pad from which to mount one's own presidential campaign). Free transportation and food for the demonstrators, as well as donations to organising groups, were instrumental in managing the business of bringing hundreds of thousands into Jakarta to demonstrate against Ahok's alleged blasphemy, in demonstrations led by radical organisations that normally play a fringe role in Indonesian society.

Once Ahok was declared a suspect in the blasphemy case, however, the contributions dried up, and radicals' subsequent efforts to convene large demonstrations flopped. Even malcontent elites do not want their hard-line hatchet men given a seat at the table.

Attendees at the rallies were hardly liberals, but nor were they mostly Islamist radicals. Greg Fealy, a leading expert on Islamic activism in Indonesia who attended the largest, ultimately peaceful rally noted that participants explained to him that they were motivated to attend by a desire to take part in what promised to be a monumental gathering of their coreligionists. They agreed that Ahok should be removed from public life, but they stopped short of arguing that religious laws should be superior to the secular laws of the Republic.

The coalition of Islamists and populists that brought down Ahok have now trained their sights on a bigger target: President Jokowi, who is up for re-election in two years. But they will struggle to replicate their success against Jokowi, who has all the financial and political advantages of incumbency and, more importantly, is of Javanese rather than Chinese heritage, and a Muslim rather than a Christian. Smear campaigns suggesting otherwise during the 2014 presidential election were ineffective, and would be even less compelling following five closely watched years as President.

That said, the Jokowi Administration has erred as it has sought to push back against the forces of populism and intolerance by giving in to their demands that Ahok be tried for his remarks, and by adopting some of their illiberal tactics.

Jokowi realised too late that the blasphemy allegations might be successfully used against his erstwhile deputy. He avoided early opportunities to dispel the accusations as a smear campaign, for fear of being seen as too liberal, and his vague pronouncements about allowing the legal process to run its course provided too much room for manoeuvre to those who would exploit that process. Although the President stepped up his outreach to Islamic leaders and other major political figures when the scope of the crisis became clear, it was too little and came too late to turn back the momentum against Ahok.

By contrast, the day before Ahok was sentenced, the Jokowi Administration announced that it would go to court to seek the dissolution of the Islamist group Hizbut Tahrir, which played a leading role in the protests. Indonesian leaders have long considered banning the organisation because it advocates the establishment of a caliphate in Southeast Asia, but have held off because it rejects violence. The decision seems motivated more by politics than law, and it will require compliance from a court system that just demonstrated its fear of confrontational Islamist groups. Banning the organisation could also drive its followers underground, where security services will have greater difficulty monitoring their activity, and may prompt its followers to reconsider their non-violent approach.

The announcement – couched in the authoritarian language of the Suharto era – legitimises the dissolution of non-violent civil society groups, a practice far more likely to be used against minorities and those advocating for a more pluralist Indonesia than against other, less tolerant groups. As with the government's recent decision to bring treason charges against a motley but largely harmless crew of activists, fringe political figures and disaffected generals who were engaged in last year's protests, its move against Hizbut Tahrir highlights the risk that the government's heavy-handedness will backfire.

Jokowi thus bears some responsibility for the predicament in which he and his compatriots now find themselves. But all is not lost. There has been an outpouring of support for Ahok from supporters of pluralism and moderate civil society since the verdict was announced. Popular support for the forces of intolerance very well may have peaked, and if starved of elite support they are likely to continue foundering.

Jokowi has been damaged by the episode, but remains in a strong position going into Indonesia's long presidential campaign. He should learn from his earlier missteps, and take a strong stand against those actively politicising intolerance now rather than later, in the political arena rather than the courts, from a position of relative strength.