I am not sure how much to read into this.... The Egyptian military is not run by the MB.... Yet....
Obama cutting back on exercises with Israel is much more telling....
Morsi (or Mursi, seen it spelled both ways) recently fired all the generals and replaced them with MB generals. Or at least more radical Islamic type generals who will be on the MB side. So I’d say that the Egyptian military is more or less run by the MB, from my very limited non-expert understanding.
They sacked the old leadership and offered them a retirement package they could not refuse. Muslim Brotherhood is Egypt now and Egypt will be Obama's Iran.