There's been rumours for a long time that Hillier and O'Connor disagree with each other quite a bit.
Now, Harper has been very quick to protect his cabinet ministers, no matter how inept. However, he's not going to shelter someone whose actions have a political cost. When the warning of that comes from one of his "old mentors" in the Calgary School, it no doubt carries a little more weight:
“Afghanistan has got to be very high on the list of problems he [Mr. Harper] has to fix,” said David Bercuson, director of the Centre for Military and Strategic Studies at the University of Calgary, as the Tories prepare for a caucus in Charlottetown this week to plot their fall political agenda.
Mr. Bercuson and other military and political experts said that there are too many voices speaking out on the Afghan military mission.
This is actually a very revealing tidbit. First, it tells us a little more about Harper's slightly irrational seeming micromanagement of his government's public face. His "mentors" at the University of Calgary no doubt spent a great deal of time and effort drilling home the idea that message is everything. (What Harper misses, in his relative inexperience as a leader, is that a good leader not only delegates, but unites his team)
The second piece of interest is the behind the scenes relationship between Harper and Gen. Hillier. Hillier has been given an amazingly free voice in the public arena - and it's obviously politicized. If Hillier is clashing with O'Connor, the only way that he would be getting that kind of freedom is if Harper was authorizing it. (Remember, everything goes through the PMO these days) In fact, Hillier's public profile is at odds with other senior bureaucrats in high profile departments who have been silenced quite harshly.
As a combination, Hillier's public profile, and the very public clashes with O'Connor spells a very short shelf life for Gordon O'Connor as Canada's Minister of Defense.
While disposing of O'Connor would be an improvement, it's not enough to salvage the Harper's government. (Especially if Harper doesn't wake up and start delegating to his team)