Put aside, for a moment, the failings of the Muslim Brotherhood during President Mohamed Morsi's one-year reign, up to and including whatever role they played in the violence that killed dozens of anti-Morsi protesters in the final days before the military ousted him power. Put aside however you might feel about the Egyptian military's decision to launch a coup, with the broad support of many Egyptians.
Focus, just for a moment, on where Egypt is right now, rather than on how it got there, important though that is. These three things are true: (1) the Muslim Brotherhood is still a big political player in Egypt, with lots of supporters and weight in society; (2) it's in the middle of an existential dilemma, a choice on whether it should continue to try to work within the system or oppose it outright; (3) the military government is cracking down fiercely on the Brotherhood, issuing arrest warrants for top leaders including supreme guide Mohamed Badie.
Those three things are a potentially dangerous combination for Egypt, and not just for the Brotherhood. The military crackdown sends a strong signal to the group and its leaders, deliberately or not, that they are not welcome in the Egyptian political system they dominated until one week ago. That would seem to make the Islamist group much, much likelier to oppose the system from the outside. And that makes Egypt's democratic experiment significantly less likely to ever really get off the ground.
The Washington Post's Abigail Hauslohner laid out the worst case scenario, writing, "For a group that has toggled throughout its history between violence and peaceful opposition, the killing by security forces of dozens of Brotherhood supporters on Monday left its members angry, embittered and at risk, analysts said, of careening toward a more militant and radicalized future."
This doesn't have to come to violence in order for it to be bad news for Egypt, including for the military that has shown every indication of wanting to be a check on Egypt's rulers but not, in the long term, to rule themselves. Think about all of those Muslim Brotherhood supporters: If they refuse to participate in Egypt's political processes or feel they're excluded, it's hard to imagine the highly activist group would just watch quietly from the sidelines. Sure, some will probably throw their support to the Salafists, who hold somewhat extreme Islamist views, but many are likely to do exactly what Egypt's non-Islamists did when they felt excluded from the Morsi government: protest, boycott and otherwise oppose the legitimacy of the government. That got Egypt to the June 30 mass protests, which got it to the July 2 coup, which now has it repeating a somewhat different version of the military-led transition that it endured – and became very quickly eager to move away from – just two and a half years ago.
Egypt's non-Islamists weren't wrong to feel they were being excluded from Morsi's government, nor were they wrong to question whether his vision of democracy was actually democratic. Whether or not you believe that the July 2 coup to remove Morsi from power was a good thing, at some point, Egypt's major political factions will have to stop opposing and undermining one another and actually work together if they want to move out of this cycle of coup-transition-powergrab-coup. Someone has to try to govern on behalf of Egypt, not just their half of it.
None of this is to deny the Muslim Brotherhood's own role in excluding huge swathes of Egyptian society during Morsi's rule and thus setting the stage for its fall from power. But the Egyptian military should understand that the Muslim Brotherhood is not the same thing as former Egyptian President Hosni Mubarak's government, which co-opted many groups but ultimately represented a small group of wealthy elites. The Muslim Brotherhood has been around for decades and it's endured some truly backbreaking oppression. Arresting Badie and Morsi isn't going to make them, their movement or the large numbers of Egyptians they represent disappear. But it is likely to turn them against the post-Morsi order, whatever that looks like. That's not something the military, the military-appointed civilian leaders or whoever succeeds them can really afford.