Some people have wondered why Egypt’s high court, doing the military leadership’s bidding, just invalidated the Egyptian parliament, even though the Muslim Brotherhood’s popularity, though strong, seemed to be on the wan. I think the simplest explanation is not that they were afraid of losing their grip on Egyptian society (though that’s probably part of the equation), but that the Egypt’s military leadership prefers not be be killed. I don’t mean this in a metaphorical sense, I mean that there was real (and probably justified) fear that a government lead by Muslim Brotherhood would lead, in very short order, to the liquidation of the military leadership. I think they were facing not one but two existential threats.
First, as shown in Turkey, when a nation’s existing military leadership also acts as an independent power base, islamists are only willing to tolerate potential threats to their own rule as long as they have to. Recep Tayyip Erdogan’s islamist AKP has moved to put vast swathes of Turkey’s previously independent military leadership on trail for blocking Islamist aims in the past. Egypt’s military is just as strong a power center (albeit one considerably less scrupulous than Turkey’s); how long do you think it would take the Muslim Brotherhood to move against the military leadership after they had consolidated power? My guess is not long at all, and the military knew it too.
Second, if we take the Muslim Brotherhood at their word, it’s obvious they’re itching for another war against Israel. And why not? They regard the “Zionist Entity” as a literal affront against God, one that must be wiped off the face of the earth. Moreover, what better way to tighten control over the levers of governmental powers than with a war against a hated enemy? There are are all sorts of ways to use “emergency wartime decrees” to eliminate opposition figures and seize direct control of businesses and ministries when everyone’s focused on the military action.
And who would bear the brunt of any war against Israel? The hated military. Win, and members of the Muslim Brotherhood government are heroes to Muslims all over the world. Lose, and it could only be attributable to traitorous disloyalty by the military leadership, which would be immediately purged.
And make no mistake about: Egypt would lose. Badly. No matter how they may try to spin the 1973 Yom Kipur War as a victory, the Egyptian military got it’s ass handed to it in all four of the Arab-Israeli Wars. The Six Day War was particularly brutal, with Israel destroying all the Arab air forces arrayed against it, most on the ground, and decisively crushing Egyptian forces in the Sinai while taking minimal casualties; they could even have taken Cairo were it not for frantic pleas of the U.S. and heavy threats from the Soviet Union. Egypt lost the Yom Kippur War as well, but actually managed to bloody Israel’s nose in the Sinai, using effective anti-tank tactics to inflict real damage on the IDF before being overwhelmed. This would be pretty much the only instance where an Arab army stood toe-to-toe with the IDF (even temporarily) until the 2006 war on Lebanon, which Hezbollah would survive despite being badly mauled.
The Egyptian military knows it would lose any war against Israel for the foreseeable future (even discounting Israel’s likely nuclear weapons arsenal), and it knows the best way to prevent one is to prevent the Muslim Brotherhood from coming to power. Strangely enough, in this instance the Egyptian military leadership is actually acting in the best interests of the nation, even if the end result also happens to be saving their own hide.