We've had that problem since General Washington was leading the troops. Look at what President Lincoln went through with his generals. Then there was Truman who had a general who wanted to be President and didn't want to wait for an election.
You know, I see an interesting correlation between Meet the Press and the discussion of the generals. Both are concerned with overturning the current order...in the Catholic Church, and in the American government.
There have been disputes between Generals and the CIC in the past, even Jimmy Carter fired Singlaub. However, can you ever recall flag officers being trotted on stage at a nominating convention to act as props for a candidate? Or a group of generals and career diplomats signing a public petition calling for the incumbent President not to be reelected and stating that the administration "justified the invasion of Iraq by manipulation of uncertain intelligence about weapons of mass destruction, and by a cynical campaign to persuade the public that Saddam Hussein was linked to Al Qaeda and the attacks of September 11?"