The Association of Social Anthropologists of the UK and Commonwealth has a very worthwhile site where there is lively discussion of the role of anthropologists (and other social scientists) in counter-insurgency. Some interesting pieces have been recently penned by Caroline Osella, David Price and Nayanika Mookherjee.
New material is being added all the time. New Mandala commentary on the 2008 Thai Studies conference in Bangkok even gets a mention!
While there is currently no major Southeast Asia focus in the Association of Social Anthropologists’ discussion, there was, of course, a time when anthropology in Southeast Asia was confronted with many of these same ethical issues. Perhaps as a sign of the times, Eric Wakin’s Anthropology Goes to War: Professional Ethics and Counterinsurgency in Thailand is now back in print.