I think there are two issues here.

The first is the petition, and its explicit assumption that anthropologists supporting COIN in Afghanistan are engaged in a fundamentally immoral activity. Here much depends on one's view of legitimacy (and in both cases, one would have thought that the fact that the missions are endorsed by both the local elected government and the UN Security Council ought to count for something).

The second issue is the tensions that arise from one's professional responsibility as a social scientist, and one's potential function as a counter-insurgent. Academic social scientists are suppose to live by a series of research ethics that, for example, require disclosure research project to most interviewees, disclosure of data and findings, informed consent, and very stringent safeguards for interviewing involuntary subjects (such as prisoners) or those otherwise unable to give informed consent. HUMINT collection, IO, PSYOPS, etc all work rather differently, as does providing professional advice in these areas. There are some potentially troubling professional and ethical implications of moving back and forth between both worlds.

I suspect most SWJ readers would take it as a given that I shouldn't divulge TS/SCI information in the classroom, even if it assisted in the noble enterprise of teaching. Also problematic, however, would be using data gathered confidentially, for particular academic purposes, and passing it on in rich detail to military/government actors with whom the interviewee would not have willingly shared it. Doing so not only violates professional ethics, but potentially endangers later academic researchers.

Frankly, its probably a good idea that professional organizations (and the military) reflect on this--and how any potential conflicts between the universes be dealt with.