Depending on what exactly what jobs you're suggesting military personnel take over, I strongly disagree, and here's why.
The problem with USAID in particular, and State political, economic, and agricultural experts in general, at least in terms of their track records in Africa and elsewhere, is that they are painfully inflexible. While NGOs have been quick to adapt to local conditions and modify their aid or assistance programs, USAID (again, in the past - not sure how they've been the last few years, but I've heard bad things) has a well-earned reputation from the days of Structural Adjustment Policies for being ideologically rigid and stubborn. The SAPs essentially said to recipient nations, "our way or we're hitting the highway with our money."
In order to be successful, economic development programs, particularly with respect to agriculture, must be tailor-made for local conditions; thus a combination of local cultural expertise and economic experience. While military personnel with experience in Iraq may be adaptable, flexible, and skilled, I doubt they will have the prerequisite skills that State really needs right now.
That said, after extolling the adaptability and flexibility of NGO aid or development organizations, I still don't think they're the answer unless we can subordinate them somehow to a unified command.
Matt
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