Egypt shouldn't become like Turkey was until a decade ago with the military calling all the shots and democracy being a weak facade.
I'm squeamish about the military taking control as well, but the Turkish military has been largely responsible for maintaining Turkey's secular governance. Perhaps they can provide that kind of leadership in Egypt as well.
Secular democratic rule > Secular military rule > Islamist 'democracy'
If the Egyptian military was comparable to the Turkish one, I might to some extent get inclined to follow your line of thought, even though I feel a democratic experiment like in Egypt should be given a bit longer than just one year to see how it works out.[
Democracy, in my understanding, also includes articulation of public opinion, demonstrations (though not riots), alliance-building, search for consensus etc..]However, the Egyptian army is among the worst institutions to lead Egypt now. The press here reported today (don't know where they got their figure from) that 40% of Egypt's wealth is held by senior army ranks, which shows how corrupt they have been and most likely are still. Army officers are also exempt from any income tax. They can pose as "defenders of democracy" as long as they want - to me it is still a bunch of corrupt hacks whose prime interests are maintaining their privileges and covering-up whatever they did during the Mubarak years.
Transparent & accountable government > partial, imbalanced Islamist clean-up > Corrupt army clans retaking control