"It appears General Hayden, was picked to make the job of CIA Director more palatable with the new rules, being all Intel Agencies now report to the Director of National Intelligence. They no longer control their own budgets, nor have a complete say in where the boundaries are drawn as to what their mission involves.
If the DNI, DIA and other military intelligence organizations begin to assume missions from the CIA, the CIA could at some point be left to wither on the vine and leave the subversive moles with dead telephones. The expanded military agencies could be staffed with vetted personnel, some of which might be transferred from the CIA. This might be the game plan and why we are seeing such a frantic effort by the shadow government to oppose it."
Your point is well taken and that might be what is happening. If so however, it is a big mistake. Military intelligence is important. So is a separate agency like the CIA. Military intelligence needs to be able to focus on strictly military matters. The military has a certain job. Military intelligence helps them do it. They also have a certain focus of expertise.
When the State Department and the CIA are dysfunctional, it is natural for the military to start trying to take over both functions for themselves. First of all however, they will not be good at them. Second of all, we don't really want our military to start to get that kind of power and scope. They should continue to play their original assigned role---to fight and win wars.
I believe Goss made a good start to cleaning the moles out of the CIA. I don't know if you recall, but he suggested quitting right at the beginning when he saw how bad it all was, and Bush encouraged him to stick with it. Lets not forget, the man is 67 years old. I'm in my mid-50s and I don't make any bones about it---age matters. I suspect he did as much as he felt he could accomplish---but the vital job of cleaning out the CIA must continue, and the vital job of cleaning out the State Department, must be begun at some point.
I agree that it would not be a good idea to roll all of the CIA's missions into other organizations. The successes of the CIA and Spec Ops in Afghanistan lead me to think that they have some very capable operations personnel. I would hope that they are also improving their intelligence gathering ability. The upper layers of the organization that process and analyze intelligence is where I think most of the problems lie. Sometimes a reorganization is a good tool to week out under-performers and that may be where Hayden's experience could be particularly useful.