Obama obviously didn't make any kind of mistake when he referred to Egypt as not an ally. He was throwing down. Here's Juan Cole, in an item headlined "Obama Plays Hardball and Morsi Folds," which fills in some interesting details:

Under Obama’s pressure, Morsi, in Brussels seeking European aid, finally explicitly condemned Tuesday’s attack on the US embassy in Egypt:

“We don’t accept, condone, or approve at all for there to be attacks on embassies, consulates or people, or killing in any way.”

“We want to cooperate with the entire world and we are cooperating now with the E.U. and the European people and with the American people and others and the U.S. administration to prevent such practices in the future. Also, we insist on the protection of persons, properties and embassies. The Egyptian people are very civilized and could not ever express their rejection of such practices with an attack on an embassy or person or consulate.”

Some of Morsi’s sudden willingness to say all this was fueled by Obama’s pressure. In addition, Morsi revealed some of his other motives:

“Muslims and Christians in Egypt are equal citizens and have the same rights… We are cautious about those principles and human values, also respecting visitors and respecting tourists… and respecting and protecting diplomatic delegations and private and public properties, and not attacking them.”

That is, somebody told Morsi he had to say something if he wanted to keep the tourist trade, much less the American alliance!

Note, please, that not only did Morsi issue an unequivocal call for protection of US personnel and property, but he expressed support for a solid Jeffersonian principle there.