Another group of thugs will be in power tomorrow.
Pretty much the army IS the government.
Obviously, every third world country is going to be ruled by crooks and thugs (come to think of it, many first world countries are too, they're just more subtle about their abuse of power).
However, some thugs are preferable to others. Would you rather have a Hosni Mubarak-style thug from the Army running things, who, while corrupt and brutal, suppresses Islamist factions like the Muslim Brotherhood and Al Quaeda fronts while protecting secularists and Christians, or a Muslim Brotherhood thug who is even more extreme and fanatical than Morsi?
The goal of US foreign policy shouldn't be supporting "Democracy" or the fantasy of western style representative governments in the Middle East. Our goal should be making sure that secular strongmen open to trade and diplomatic relations with the US rule these nations.