I am sure he does as long as those pesky civilians do not cancel the peace treaty with Israel or give military support to the Palestinians etc. With the generals the U.S. has the option to limit these kind of adventures. It should be said that the leader of the Muslim Brotherhood Mohammed Mursi already states that is not his goal to do any of this. But we have to be realistic, especially under Nasser the Muslim brotherhood was persecuted by the army. They are not friends. So distrust will remain on both sides and the military will not be willing to give up power to them. And the U.S. will not be willing to push their “allies” to do so imo.
Egypt has lots of problems and could use the money, but traditionally it had been used to fill the coffers of the army and their power base. How in the future these funds will be used will depend on Congress and their assessment of the political development in Egypt.
Indeed many of the early protesters were quite more liberal than the Muslim brotherhood. But the voters in Egypt did not trust their westernized brethren either.
But all sides are aware that in a civil war things could go from bad to worse. Sectarian and religious divisions could lead to a catastrophe like we saw developing in Syria.
It seems the Muslim brotherhood is aware that another revolution would mean that the army and their more liberal supporters would choose to fight. The best case scenario imo is to copy the Turkish development of a Muslim democracy were the military initially had a veto option while the civilian government ran most of the day to day business except for military and foreign policy affairs. Its not perfect but from the perspective of the brotherhood quite better than the old status quo.