The election of a Muslim Brotherhood leader to the presidency of Egypt arrived in Israel like delayed thunder after a burst of lightning: It was not a surprise, but it still provoked nervous attention.

Mohammed Morsi, Egypt’s first democratically elected president, comes from an organization that has a long history of opposition to peace with Israel and even to the very existence of the Jewish state. And yet, the situation may not turn into a disaster — at least not any time soon.

In the face of uncertainty, there is time for Israel to prepare for the worst. Israel must remain strong. But for those willing to contemplate a glass half full, there is a possibility that this could turn out well.

An early report from Iran, claiming Morsi had promised to revise the peace treaty with Israel and forge a strong relationship with Tehran, was quickly denied by the Egyptians as completely false. That was the first sigh of relief for a very tense Israel.

For now, Egypt’s military remains in control of foreign and security policy. Eventually, however, that could change, as Turkey’s example shows.

But even if Morsi had control of foreign policy now, it’s worth remembering that one of the Muslim Brotherhood’s main traits is patience and pragmatism. The Brotherhood, whose membership Morsi has now resigned, knows exactly the pan-Islamic future it wants to achieve, but it adheres to a timetable that is thoroughly unrecognizable in the earthly world of politics. The Brothers waited decades for this moment, and they are not about to squander it.

The Muslim Brotherhood and Morsi have made no secret of their wish to see Islamic law, Sharia, become the law of the land in Egypt. But they say they will wait until the country is ready. They may secretly want to end peace with Israel, but they will push no such plan before it’s time.

In the new Egypt, popular legitimacy matters, and that means righting the economy first.

Egypt has many pressing problems at the top of its agenda. Starting troubles with Israel would make many of the problems worse. Egypt desperately needs the $2 billion a year it receives from Washington, and tampering with the peace treaty could bring an end to aid. It could also threaten urgently needed foreign investment and tourism.

Morsi’s first speech did not mention Israel but he spoke of a “message of peace,” with a promise to respect international agreements, code for the Camp David Accords.

The new Egypt is a work in progress, with powerful forces pulling in different directions. The country has become more open to debate and new ideas. Already, occasionally, the extremely rare pro-Israel voice of an Egyptian activist can be heard through the noise. It’s true.

Nobody knows what the future holds for Egypt or for relations with Israel. But, as I have written before, Israel’s peace with Egypt has always been dangerously fragile, precisely because it was not peace between two countries but between one country, Israel, and one regime, the Mubarak dictatorship.

Mubarak allowed anti-Israel sentiment to fester, despite the peace agreement. If this period of transition manages to bring relations between Israel and a president who represents a wider segment of the population, it could lead to relations that become more stable and reliable. Still, there is no denying that relations will change.

Israel will not count on the support it enjoyed from former President Mubarak in sealing the border to contain Hamas in order to slow weapons transfers. But Israelis would not object to having Cairo take more responsibility for supplying Gaza with other provisions.

Morsi’s election was greeted with jubilation in Gaza, which is ruled by Hamas, a branch of the Muslim Brotherhood. The celebratory machine gun strafing of the sky left one dead and three injured there.

The Brotherhood’s success will limit Israel’s freedom to respond to Hamas. That’s why recent weeks have already seen dozens of rockets fired into Israel from inside Gaza.

Eventually, temptation to blame Egypt’s problems on Israel may return. And the Palestinian issue, too, remains combustible. But it’s not in Cairo’s interest to tamper with Israel now. (Just in case, Israel remains far stronger militarily.)

The horizon can look ominous, and perhaps that lightning means that storm clouds really are gathering. But clouds do occasionally come with silver linings.