From an Anthropological Perspective
There has been a debate that has been going on for years among social scientist, in particular anthropologists. Should anthropologists cooperate with the military (or any other government organization for that matter)? The negative side points out that anthropology was created as a colonial tool (to put it bluntly) and that as a discipline, they should repudiate all such work. The affirmative side argues (1) pretty much everything in applied anthropology causes effects on the society examine, whether on behalf of corporate interests, or non-profit (whose motives don't always look much more noble then the colonial white-man's-burden) (2) the negative side seems to imply that anthropology should not be used to mitigate or prevent cultural damage. If they can't do that, what is the use of anthropology (other than for corporations to exploit people or non-profits to manipulate a society)? I'm being slightly simplistic here. The link provides a much more nuanced view. Searches for 'anthropology' and 'military' should find articles in the New York Times, the BBC and various anthropology and military sites.
In one sense, the issue is somewhat moot. The military (at least the American tradition) is bound to fill the mission given to it by its civilian leaders. If accomplishing that mission is best done by having people study the society that exists in the environment to avoid the use of destructive force when it can be avoided, the military would do so. Whether or not people who have the word "anthropologist" in their resumes are involved is quite irrelevant. Even if it would make things easier if there were some at hand. (if not, the military will make do with who they can find who is available.)
There is a bigger question on the anthropologists side. What is the role and substance of ethics? Is ethics an avoidance of labels that don't sound nice? Is ethics a list of "thou shalt nots." Are both the ends and the means irrelevant, if the perceived "ultimate end" is "wrong" (the quotes are because the "ultimate end" and "wrong" are not as defined by the doer, but by an uninvolved party who has noone's interests in mind, namely the anthropological profession, which is divided.)
In general, this is probably the problem with ethics, especially as practiced in non-practitioner settings. Ethics tends to be discussed as what is wrong, not what should be done. In other words, what not to do. And the principles that are seized on to decide the what not to do become absolute and definitive. To the exclusion of all others. Including human life. In my interaction, people will hold to these principles even when the life that is to be lost has been identified (which is the case here as well.)
For many professions, the focus of training is on what (and how) to do. In an environment where everything is focused on acting, negatively based ethics quickly becomes irrelevant. (i.e. the U.S. Army will study the cultures it works among to determine non-destructive ways of solving conflict, regardless of the collective decision of the anthropological community.) And the members of the academic disciplines that would prefer to actual engage their world for positive ends, rather than withdraw to avoid breaking rules, or look for areas of activity that are not addressed (such as social anthropology by marketers and advertising), are faced with professional isolation, or creating a new profession.