I know people are all in shock over the crackdown on the Muslim Brotherhood in Egypt but seriously, what else could the Egyptian military done? They really had 3 options:
1. Allow the protests to continue unmolested
2. Do what the Obama administration and the EU has been pushing for and allow the Muslim Brotherhood back into the government either immediately or through a future election
3. Clear the protests and aggressively suppress the Muslim Brotherhood
The first choice does sound appealing but in the long run it clearly wouldn't have worked. First, it would make the military look weak and unwilling to do what needs to be done. The Brotherhood would have become more and more aggressive over time, seeing where the line actually was, making the military look even weaker if they continued to do nothing. Plus, as the economy is likely to continue to be weak thanks to the second Revolution in a year, the Brotherhood protesters would soon be joined by more secular anti-Mubarak and anti-Morsi protesters who would be upset by the economic situation more than anything else. As the numbers would swell, we would see a repeat of the last two revolutions. And if the military waited until then to have a crackdown, it would be an order of magnitude bloodier than today's.
The second choice is also a non-starter. In the west we are used to losers in elections simply coming back for the next one or start to make real money on the speaking circuit. That is not the way it works in the middle east (outside of Israel of course). Losing power can lead to losing your life or your freedom. The military simply can't risk giving up power at any point to the Muslim Brotherhood, not after the recent coup. And don't think the military has missed the actions of the Islamist President of Turkey. He recently purged 250 military men, politicians and journalists claiming they were planning a coup and the former head of the armed forces just got life in prison.
That leaves us with the third choice, which clearly from the military's point of view is the least bad option. Will it radicalize elements of the Muslim Brotherhood? Sure, but they really are only capable of terrorism, not a sustained guerrilla campaign and hence not much of a danger to the military in charge. The military can probably hold power almost indefinitely as long as there are no mass unit defections and the US & EU don't mess things up and force them to share power with the Brotherhood.