Among the biggest losers from the current Arab political upheavals are the Christian minorities of the Middle East.

Long before the Arab Spring, Iraq’s historic Christian community had shrunk dramatically, as tens of thousands fled threats and bomb attacks by hardline militias. The flood of refugees pouring out of Syria includes many of that country’s Christian minority, who fear a radical hardline takeover if President Bashar Al Assad falls.

Meantime, most of Egypt’s Coptic Christians, who make up 10 per cent of the population, are deeply worried by the election of Muslim Brotherhood leader Mohammed Morsi as president. “There is a feeling that democracy has been a disaster for us,” says Samia Sidhom, managing editor of Watani, a newspaper that serves the Coptic community. (The Coptic church dates back 19 centuries and is based on the teachings of St. Mark, who took Christianity to Egypt.)

What Morsi does, or doesn’t do, to reassure Copts will reveal whether Christians can enjoy equal rights in an Islamist-led Egypt – and will hint at their likely fate in Syria as well.

“At the beginning, Copts had a lot of hopes (in the revolution),” Sidhom told me during my recent visit to Egypt. We sat in her cramped office, which was filled with old computers and worn furniture and was not far from Tahrir Square, as she worked on the next issue of the weekly.

There were simmering sectarian tensions under the Mubarak regime, including attacks on the Copts’ places of worship. To open new churches, Copts were required to get presidential permission, which was rarely forthcoming, forcing them to worship in “unlicensed,” and thus vulnerable, structures.

“We thought the revolution would solve our grievances,” Sidhom said, ruefully. “It took a lot of people by surprise that Islamists were able to take advantage of the revolution.”

Under Hosni Mubarak, she said, despite the problems, ultraconservative Salafi Muslims had no power. Now, young Salafis return from the cities to their home villages, where Copts and Muslims have lived side by side, and warn them against Christian “infidels.” She reeled off a list of churches that have been burned down since the revolution.

Some of these churches were rebuilt by the Egyptian military, including one I visited in the working-class Cairo district of Shoubra. But the military carried out a brutal attack on peaceful Coptic demonstrators near Cairo’s Maspero television building in March, which has left many Copts embittered. More than 20 demonstrators died, some deliberately run over by military vehicles.

Now that Morsi has won, Copts feel there will be even greater discrimination. Sidhom believes Christian women will face social pressure to veil and expects more government pressure to close unlicensed churches.

The biggest threat – the one that most terrifies Copts – is that the new government will push to enshrine Sharia law in the constitution. At present, it is the Salafi-oriented Nour party that is demanding the specific application of Islamic law.

The Muslim Brotherhood’s Freedom and Justice Party still supports the current, more vague, provision in the current constitution, which says Sharia “principles” should be the basis for law.

However, Sidhom believes the Brotherhood will ultimately apply a conservative form of Islam, in which “there is no national Egyptian identity,” but rather an emphasis on a pan-Islamic community. This, she says, would foreclose equality for Copts or other minority groups.

Morsi and the Muslim Brotherhood talk a good game about inclusivity. But few Copts – or moderate Egyptian Muslims – have forgotten that in 2007 he drafted a Brotherhood platform that specified that no Copt or a woman could become president. (After an outcry, this platform was withdrawn.)

If he genuinely wanted to demonstrate good faith towards Copts, Morsi could take concrete measures to prove it. First, as a new Human Rights Watch report suggests, he could end the Mubarak-era impunity for incidents of sectarian violence. If Egyptian authorities finally punished those responsible for notorious attacks against Christians, and arrested those responsible for the Maspero deaths, it would set a new tone in the country. If the president ended the restrictions on building churches, Copts would have renewed hope.

Many doubt that Morsi is ideologically capable of such enlightened positions (which is why members of the community voted heavily for the presidential candidate backed by the army, Ahmed Shafiq, and why they support a continued strong military role behind the scenes). There’s no doubt the president would face intense pressure from Brotherhood hard-liners and from the powerful Salafis.

But Morsi’s presidency will be defined by how he deals with the Coptic minority. This will show whether he grasps the meaning of pluralism and democracy and wants a modern country. The West should press for such pluralism, and make aid contingent, but it cannot force him.

“Morsi will go forward with Islamicisation,” predicts Sidhom, pessimistically. I’d say the odds favour her prediction. Does Mohammed Morsi have the vision to prove us wrong?