To anyone interested in the future of anthropology as an academic discipline/profession, this vigorous debate over whether or not anthros should be working for the military in Iraq and Afghanistan is fascinating:

At issue is a longstanding code of ethics for the discipline, one which decrees that anthropological research should never be used to inflict harm, must always have the consent of the population being studied, and must not be conducted in secret.

The debate over the role of anthropology in national security is expected to come to a head next month in an American Anthropological Association report examining the ethical questions of cooperating with the military.

...

The military's own descriptions of the new teams give pause to Price and others - such as one Pentagon official who likened them to the Civil Operations and Revolutionary Development Support project during the Vietnam War. That effort helped identify Vietnamese suspected as communists and Viet Cong collaborators; some were later assassinated by the United States.

Simply put, the question isn't whether or not having Army anthropologists is good for the Army or whether or not the Iraqis/Afghanis studied by them will be irreparably harmed. The question, in my mind at least, is limited to whether doing this sort of thing is so destructive to the practice of anthropology that it makes it not worthwhile in the long term.

And at the risk of being overly critical, I'd suggest that if anthropology had done a better job in the last several decades making a clear case for what the purpose and use of the discipline is, they would have a better argument for what they do needs to be protected and not mucked around with.