My main point of note, is that in spite of all the talk about Muslim-this, and Sharia-law that, it seems pretty obvious why he wasn't allowed to continue on.
Army Ousts Egypt’s President; Morsi Is Taken Into Military Custody
David Kirkpatrick, New York Times, 3 July 2013 (hat tip: Early Warning)
For Mr. Morsi, it was a bitter and ignominious end to a tumultuous year of bruising political battles that ultimately alienated millions of Egyptians. Having won a narrow victory, his critics say, he broke his promises of an inclusive government and repeatedly demonized his opposition as traitors. With the economy crumbling, and with shortages of electricity and fuel, anger at the government mounted.
If he had been able to keep the country running, he would still be there. Arab Spring was a response to population pressures, Middle Class self interests, and an inability to keep subsidizing the lifestyles of people. When military budgets got cut by former life-time President Hosni Mubarak, the military stepped aside and let things run their course. It looks like the military has decided to step back int.