[WS:] No doubt. But to lay hold on these institutions, they need to have institutional framework in place (unions, organizations, political parties, etc.) - which I believe is Gramsci. I may be wrong, of course, but I simply do not see any such institutions in Egypt, not even Muslim Brotherhood. Do you?
Furthermore, "switching sides" does not mean that the military suddenly switched to the people's side (whatever that means.) It seldom, if ever does. It simply means that it withheld its support of the current regime and put its bets on someone else - which is exactly what seems to happen.
Finally, movements are of course important (pardon my earlier quip,) but by themselves they are insufficient to grab the state power, let alone implement institutional changes that you mentioned. In a typical scenario, they tip the balance of power toward the reform-minded institutional actors, and if conditions are right, this may allow those reform-minded institutional actors grab state power. I think it is too early to say whether that is what happened in Egypt - but if it did, the only institutional actor capable of such a feat in Egypt was the military (or its faction) itself. That may not be exactly the revolution many were hoping for, but then who knows. Remember Portugal?
Wojtek