Let’s get this part out of the way right at the beginning: I support the ouster of the Muslim Brotherhood in Egypt by the military and the anti–Muslim Brotherhood coalition, including the masses of people who took to the streets to demand his resignation, and who cheered the coup-makers.

That said, there needs to be a long list of caveats, the first of which is that Egypt’s armed forces need to allow civilians to run the show henceforth, by writing a new constitution, electing a new parliament and president, giving free rein to the media and civil society, and giving the Muslim Brotherhood an opportunity to reclaim its space in Egypt’s political life.

The military, which in 2011 thought it had a deal with the Muslim Brotherhood, now thinks it can strike a deal with the non-Islamist opposition forces that opposed Morsi. Maybe it can, but the opposition’s task now is to corral the generals and create lasting political institutions that can eventually transforms Egypt’s version of the Pentagon into a force subservient to civilian rule. That could take years, and if the generals try to hold on to political power now it might mean that yet a third Tahrir Square–style mobilization will be needed.

Those horrified by the military’s takeover, who worry about Egypt’s “deep state” of military, security and intelligence services, must also recognize that the security establishment didn’t go away in 2011, when the government of Hosni Mubarak was ousted. It’s been there all along, during the transitional phase when the Supreme Military Council ran the show, and then during the presidency of Mohammed Morsi, the stand-in for the secretive Muslim Brotherhood leadership. Indeed, it’s odd that many of the same people who called the fall of Mubarak a “revolution” today call the fall of Morsi a “coup d’état.” In fact, both events followed almost exactly the same pattern: a mass mobilization creating an virtually ungovernable state of affairs in Egypt, followed by a military action to oust the leader.

One difference, of course, is that Morsi was elected. Lawyers can argue about the importance of that fact. If elections are all that matter, then the supporters of Morsi have a point when they say that the “legitimacy” of Morsi’s rule has been trampled on. But his government routinely violated that legitimacy by a series of high-handed actions that sparked the very protests that led to his downfall. And while it would might have been preferable had Morsi’s rule fallen under its own weight, in parliamentary and then presidential elections to come, that’s water under the Nile River’s bridges.

Now, once again, Egypt has a chance to get it right. That’s the view of Mohammed ElBaradei, the former chief of the International Atomic Energy Agency, who emerged in post-Mubarak Egypt as one of the leaders of the new politics. ElBaradei took to quoting a baseball philosopher:

“We just lost two and a half years. As Yogi Berra said, ‘It is déjà vu all over again,’ but hopefully this time we will get it right.”

Still, ElBaradei erred badly in defending the preemptive arrest of Islamists since Wednesday. It’s true that the Muslim Brotherhood and its allies might choose insurrection now that they’ve been ousted, but until that happens there’s no reason to round them up a la Mubarak. According to the Times:

Dozens were arrested, including Mohamed Badie, the group’s supreme guide; his deputy, Rashad Bayoumi; and the head of its political wing, Saad el-Katatni. Also on the wanted list was Khairat el-Shater, the group’s powerful financier and strategist.

Make no mistake: the Muslim Brotherhood are not the good guys. Since its founding in 1928, it has taken the form of a secretive, often paramilitary cult, with a cell-based structure, an anti-democratic ideology, and a steely determination to impose on society its benighted vision of ultraconservative Islamism. For eighty-five years, the Brothers have staunchly opposed nationalism, Nasserism and Baathism, socialism and communism, and liberalism in all their forms. Like Saudi Arabia’s leaders—with whom the Muslim Brotherhood has had its differences over the years—they’ve often seen Zionism and communism as twin parts of a worldwide conspiracy against Muslims—and by Muslims, both the Saudis and the Muslim Brotherhood mean orthodox mainstream Sunni Islam, not the Shiites. As for democracy well, the Muslim Brotherhood is not a fan. In today’s paper, The New York Times quotes a Muslim Brotherhood supporter thus:

“Didn’t we do what they asked? We don’t believe in democracy to begin with; it’s not part of our ideology. But we accepted it. We followed them, and then this is what they do?”

And, although it’s highly unlikely that the Muslim Brotherhood in Egypt can spark the sort of civil war that plagued Algeria after that country’s military ousted an elected Islamist government in 1992, the Times reports that some backers of Morsi may be rallying for “jihad”:

In Egyptian Sinai just hours later, thousands of Islamists rallied under the black flag of jihad and cheered widely at calls for “a war council” to roll back Mr. Morsi’s ouster. “The age of peacefulness is over,” the speaker declared in a video of the rally. “No more peacefulness after today.”

“No more election after today,” the crowd chanted in response.

It’s troubling, and a mistake that ought to be corrected soon, that the military has issued arrest warrants for hundreds of Muslim Brotherhood officials. The new, transitional civilian president, a former judge, is apparently opposed to that crackdown. And the leadership of the opposition movement that mobilized anti-Morsi forces over the past several months has gone on record saying that Egypt’s political society has room for all, including the Muslim Brotherhood.