IMHO the military has always been in charge in Egypt. They let Mubarak be the figure head as long as he stayed out of their money making operations. And they were pretty quick to let him go after 30 years when it was convenient to appease the masses.
I think the Egyptian military will do whatever it takes to keep its power. If that means they'll have to murder the Muslim Brotherhood by the hundreds or thousands, they will.
Civil War in Egypt? A good possibility exists because the Muslim Brotherhood is closer now to power than they ever have been. They're not receptive at being told “No. Now is not the time.”
If the military stays in power, that will be better than hving the Islamists take over. But can they? The Generals in Turkey, who had run the country for almost a century, let the Islamists form a government, and now the Islamists are in control and some of the generals were jailed or executed.
And meantime, the Generals are giving the Islamists a free hand at burning churches and murdering Copts, and even helping them out. Not good. Far better if Mubarak had passed things along to his son, with the Generals controlling things in the background.
Thank you, Obama, for enabling this bloodshed.