What do you consider the real issues at stake?
I suspect Morsi is/was preparing a strike against Israel, quite possibly it had been green-lighted by Obama. The Egyptian military wants no part of this, at least not now, since with the trouble in Syria, Israel is going to be hypervigilant.
I believe Morsi thinks the chaos in Syria works to his advantage in a strike against Israel, but the military is of the opinion it is too big a gamble, presently.
Morsi's position became a bit more complicated with the release of a Lybian document naming Ansar al Sharia, the Muslim Brotherhood, and himself personally as involved in the attack on the Benghazi Consulate, and the subsequent death of Ambassador Stevens. I don't think that the Egyptian military was advised of this little adventure, and they are none too happy about it. I suspect they view Morsi, and the Muslim Brotherhood, ideologues all, as being too reckless to remain in power, and are secretly working with the opposition to achieve his ouster without too much fuss, soonest...
the infowarrior