Is Egypt facing an "existential crisis" between the forces of Islam and secularism?

This may be the week, month or perhaps even year in which the world decides how it must deal with the Islamic uprisings in failed states, struggling states and historic states like Egypt. Today, reports form Cairo indicate that the government (read military) is actively considering banning the Muslim Brotherhood. After some 80 years of being "banned" under dictators Nasser, Sadat, and Mubarak, Egypt held "free" elections a year ago, in which a member of the Muslim Brotherhood was elected president.
Mohammed Morsi allegedly overstepped his authority by declaring himself to be above the constitution a document slanted heavily in favour of the establishment of an Islamic state. Morsi was overthrown by the military only weeks ago, in what the U.S. is refusing to define as a "coup" and subsequently Morsi's followers have taken to the street in protest. Today they have taken refuse in a Cairo mosque with the military firing both tear gas and live ammunition into the building in an attempt to rout the Brotherhood from its "sacred refuge". Brotherhood members have allegedly been firing back in which is obviously calculated to generate as much negative publicity for the "government" as possible.
One analyst, a professor in the London School of Economics on Middle Eastern issues, today told CBC Newsworld reporter/host Nancy Wilson that he sees the struggle as an "existential struggle" for survival between the Islamic forces (the Brotherhood) and the secular forces, the government/military. He sees this conflict which could easily become an all-out civil war as determinative of the kind of state Egypt is going to become in the future. On the other hand, the former Prime Minister of Israel, Ehud Barak, interviewed by Fareed Zakaria for his Sunday public affairs program in CNN, Global Public Square (GPS) tells Zakaria that the world should support Sisi, the head of the military, as the best hope for the long-term stability of both the Middle East and the state of Israel. Already, conservative pundits in the U.S. are dubbing this the Obama administration's greatest foreign policy failure.
Confusing, complex, and troubling would be mild adjectives to describe the situation.
Dangerous would also seem applicable.
From the London Telegraph today:

Al-Qaeda head Ayman al-Zawahiri accuses US of plotting removal of Mohammed Morsi in Egypt

Al-Qaeda head Ayman al-Zawahiri has accused the US of "plotting" with Egypt's military, secularists and Christians to overthrow Islamist president Mohamed Morsi, in an audio recording posted on militant Islamist forums.

In his first public comment on the July 3 military coup, the Al-Qaeda boss, himself an Egyptian, said: "Crusaders and secularists and the Americanised army have converged ... with Gulf money and American plotting to topple Mohamed Morsi's government."

In the 15-minute recording, Zawahiri also accused Egypt's Coptic Christian minority of supporting the Islamist president's ouster to attain "a Coptic state stripped from Egypt's south."

Zawahiri attacked Vice President Mohamed ElBaradei, the Nobel Laureate and former UN nuclear watchdog chief who was an opposition leader during Mr Morsi's single year in office.

Mr ElBaradei is the "envoy of American providence," Zawahiri said, labelling the former International Atomic Energy Agency chief as "the destroyer of Iraq."

Zawahiri, who belonged to the militant Egyptian Islamic Jihad group, criticised Morsi's Muslim Brotherhood movement for going soft on applying strict Islamic law.
What the piece in the Telegraph did not mention is that Ayman al-Zawahiri has a brother in the Muslim Brotherhood, Mohammed al-Zawahiri, and it would seem both reasonable and predictable that such a powerful link would and could lead to further linkages between the "Brotherhood" and the AlQaeda network currently operating in Syria, as well as in many other countries in the Middle East and Northern Africa.
If the professor from the London School of Economics is right, that this struggle is perceived by both sides as an "existential" struggle for survival, then we  could be witnessing the first formal, open and
perhaps most dangerous theatre in the AlQaeda terrorist movement against the U.S. specifically and the west generally.
While urging the European Union, and not the U.S., to become a bridge between the two opposing sides in the Egyptian conflict, the professor openly acknowledged the declining influence of the United States in the current maelstrom.
Banning 10% of the Egyptian population from participating in elections, public discourse and debate at the official levels, would be analogous to banning all books that disagree with the theological dogma of a particular church, or the banning of all public media that openly criticizes the government, or banning all alcoholic beverages in the age of prohibition: IT SIMPLY WILL NOT WORK!
It will drive the highly organized "Brotherhood" underground into multiple, dangerous and less easily identified and detected cells of violence, in a movement whose tentacles already reach into the streets of dozens, if not hundreds of nations around the world. It will also instantly invoke "martyrdom" status on the organization, a status that carries with it the promise of an eternal life of considerable pleasure, if reports from earlier incidents are to be given credence. And it will provide another powerful recruiting instrument which they can and will deploy in their determination to form a caliphate across much of the world's map. Such a development will not and cannot develop without the preferred instrument of violence already demonstrated to be the preferred methodology of AlQaeda attacks in many countries.
We are sitting on the edge of our chairs, anxiously awaiting the intervention of serious, credible and powerful mediation from the world leadership community. The United Nations, the European Union, the United States, the Arab League.....they all have a deep and incontrovertible and permanent stake in the outcome of the Egyptian burgeoning civil war...as do we all. And our interests are not merely economic, as in tied to the provision of  energy products which could be imperiled if the conflict grows. Our interests are in reaching a permanent, sustainable, balanced entente between the forces of secular governance and the Islamic forces of Sharia law around the world...and that means in individual nations where poverty and political unrest play into the hands of the Islamic terrorist movement.
We are all sitting on the very close sidelines to a conflict whose boundaries can envelop not only the people of Egypt, Syria, Somalia, Nigeria, Mali, and many other obvious targets, but could infect the conversations among all nations of the world, if they have not already achieved that goal. The world cannot tolerate important conversations about poverty, climate change, the provision of health care and education to all corners of the planet to be contaminated by this existential struggle between the forces of Islamic caliphate and the forces of secular governance.
This may well be a "red-line" that has declared itself, without a single political leader having set it as the agenda for his/her nation's agenda.