I agree that the Egyptian military coup waas "good" as far as military coups go.
However, some things to consider:
Morsi's supporters. Whilst the Army had the Brotherhood leaders in dungeons for a century they now have proven popular support, regular clashes with the "moderates" and now that Morsi's dictatorship lacks military support it looks like the Brotherhood will use affiliated groups to commit acts of terrorism against the government(funded/trained/unleashed by other states, possibly just with the intention of destabilising the government,) whilst keeping layers of distance/deniability from these groups. They've(the Brotherhood) waited and survived a century for power and they're not just going to hand it over because the military doesm't support them.
The Egyptian military doesn't have the same sort of secular history that the Turkish military has. Basically they(Egyptian military) realise that right now their best bet is to keep getting Western money and military support, however their ultimate aim is clearly Israel; The Sinai their stepping stone. Who just killed several dozen Israeli border guards? Must have been one of those terrorist groups in the Sinai that the military can't control. In the same way the Pakistanis can't control the Afghan Taliban.
How will the hardliners of Egypt react to going back to a military dictatorship that won't confront Israel(yet)?
Is there an Islamic faction in the military? It Zawahiri's unit that killed the president during a military parade as I'm sure you know.
These are just some of the complications that come to mind. I'm sure you know a great deal more than me on the subject and I'm interested in your take.
EDIT: THey(the Islamists) have safe haven in the Sudan of course which is where much of Saddam's non-existent chem/bio weapons ended up via Syria.