The Obama administration’s call for an “inclusive” political process in Egypt with a role for the Muslim Brotherhood was all but overtaken by clashes in the streets of Cairo.

Violent protests today over the military’s ouster of President Mohamed Mursi raised fresh doubts about prospects for an eventual accommodation that would let the Islamic organization that backed Mursi compete in new elections.

While President Barack Obama’s administration has stopped short of condemning the July 3 military takeover, it has called on Egyptian leaders to pursue “a transparent political process that is inclusive of all parties and groups,” including “avoiding any arbitrary arrests of Mursi and his supporters,” Bernadette Meehan, a spokeswoman for the National Security Council, said yesterday in a statement.

The administration has urged the Egyptian military to stop using heavy-handed tactics, according to two U.S. officials who asked not to be identified commenting on the private communications. They said the administration is concerned that some in the military may want to provoke the Islamists to violence and provide a rationale for crushing the movement once and for all.

Such a move would fail and probably prompt a shift to al-Qaeda type terrorist tactics by extremists in the Islamic movement inEgypt and beyond, the U.S. officials said.

Three people were killed and 20 people injured today outside the Republican Guards headquarters in the capital, Health Ministry spokesman Yehya Moussa said by phone. Security forces there fired at pro-Mursi demonstrators attempting to march on the compound. An additional two people died in North Sinai, Moussa said.

Leadership Crackdown

The Muslim Brotherhood had appealed for peaceful demonstrations following the crackdown on its leadership, and its supreme guide, Mohammed Badie, spoke at a pro-Mursi rally, denying reports in state-run media that he had been arrested. The military-appointed government had said it would respect such protests.

Locking out the Muslim Brotherhood from the early elections promised by the military “would be a cure worse than the ill, almost certainly driving Islamist groups underground and giving rise to a generation of radicalized Islamists, in Egypt and beyond, who will have lost faith in peaceful, democratic change,” the International Crisis Group, a New York-based organization that offers recommendations to policy makers, said in a July 3 statement.

A crackdown on the Brotherhood by Egyptian authorities in the early 1950s contributed to its radicalization. After an army coup ousted Egypt’s monarchy in 1952, the Brotherhood was accused of trying to assassinate the president. The party was banned and thousands of its members were tortured, imprisoned and held for years.

Al-Qaeda Links

Members of the group counseled a young Osama bin Laden in Saudi Arabia, and Khalid Sheikh Mohammed, the architect of the Sept. 11 attacks, was a member of the Brotherhood before joining al-Qaeda. Ayman al Zawahiri, the current al-Qaeda leader, also was a member.

The Brotherhood faced repeated crackdowns under successive Egyptian presidents until the revolt that led the military to topple authoritarian President Hosni Mubarak in 2011 opened the door for it to compete and win a democratic election.

Now “the Islamists feel very much that they’ve been deprived of a legitimately won election” said Michele Dunne, who heads the Middle East program at the Atlantic Council, a Washington policy group.

Violent Allies

While the Brotherhood hasn’t used violence in a long while, Dunne said in an interview, “some of their allies — Salafi or jihadi groups — could turn to violence” more readily, she said.

The Obama administration has avoided describing the military takeover in Egypt as a coup because that could force a cutoff in $1.55 billion in annual U.S. aid to Egypt. A U.S. law bars “any assistance to the government of any country whose duly elected head of government is deposed by a military coup d’etat or decree,” or a coup “in which the military plays a decisive role.”

The administration previously has sought to avert provisions restricting aid to Egypt. In March, the State Department let assistance continue despite conditions imposed by Congress that the country demonstrate democratic progress. The State Department cited national-security interests, while administration officials also said the potential loss of thousands of U.S. jobs was a consideration.

IMF Loans

Suppression of the Brotherhood also would raise new doubts about Egypt’s continuing efforts to negotiate terms of a possible $4.8 billion loan from the International Monetary Fund.

An IMF spokeswoman, who asked not to be further identified, said in an e-mail on July 1 that the fund was following developments closely. The spokeswoman reiterated the IMF’s call for Egypt to develop and implement a homegrown program to resolve economic and financial challenges facing the country.

As Egypt seeks a transition to democracy, it’s hobbled by the lack of a road map to follow, according to Amy Hawthorne, a senior fellow at the Atlantic Council and a former State Department official who worked on the country’s transition after Mubarak’s ouster.

First, the military made an arrangement with the Islamists to the exclusion of other groups in Egypt, she said.

“Now we might see the military doing a deal with non-Islamist groups and excluding the Islamists,” Hawthorne said. “The only way Egypt is going to be able” to establish democracy “is if all groups agree on the basic rules of the game.”