I dont know what Fog meant by that comment, so I won't speculate, but there may have been some inadvertent truth to his statement...
Petraeus may not want to run for political office, but that doesn't mean he couldn't be a political threat.
I dont know what the Generals politics are but with the 2012 election coming up the President may have wanted to take him out of the equation... Imagine worst case for the President the General, after having retired from the Army just ahead of the election, becomes very critical of the Obama administration and is outspoken. VERY Damaging.
Medium / bad case scenario the General endorses the Republican nominee. Public opinion of the General has been pretty high, that could sway A LOT of voters, and you can bet CNN, FOX, MSNBC would be all over that endorsement.
As CIA director he is off the board so to speak...