One is that the DoD, CIA, etc are coopting others' scholarship, tactics and organizations when it suits their purposes.

As usual.
The range of possibilities you suggest should, in fairness, include the option that Gene Sharp is just what his writings themselves seem to indicate.  The best way to evaluate that option is to read a piece or two of his writings, to sample fairly his ideas.
That's the position I have arrived at.

Then ask yourself if they lend themselves to CIA destabilization efforts.
I think, if I were an agancy analyst, I would see utility in his work. So --yes, I agree that co-option  could easily be happening, even likely.
I do not, however, find an iota of evidence that Dr. Sharp has himself willingly aided any project of any of the alphsabet soup purveyors of perfidy and cynicism. The symbol of Jesus has been co-opted for truly evil purposes.
But Sharp's tactics are, in the end, far more of a hazard for the agency than an asset, I think. If so, then what the signers of the letter above saw as a campaign of character assasination also makes sense.
The two positions are not mutually exclusive. at all, and are in fact common in the Machiavellian world of spooks.  

Capitalism searches out the darkest corners of human potential, and mainlines them.