I don't think it counts as dark side epistemology. As one of the anthropologists opposing the change was quoted in the Psychology Today article as saying, it's more a matter of cultural anthropology coming to see itself as a kind of esoteric journalism than a rejection of empirical data as such. It's also part of an ongoing intradisciplinary conflict between cultural anthropology and the other three fields of anthropology: archaeology, biological anthropology, and linguistics. The Chronicle of Higher Education article is a little clearer and less polemical than the PT blog cited, though the author has his own credibility problems.
It's entirely possible that the end result will be the Society for Anthropological Sciences seceding, and the AAA won't be the professional association for anthropologists anymore. It's already the case that archaeologists and biological anthropologists rarely attend the AAA annual meetings.
Taboo "science" and "rationality"! Replace the symbols with the substance!
(Uttered as mindless slogans, to set the atmosphere.)
Since there are already factions identified as scientific and not, I don't think faction not identified with the word feels guilty about the lack of identification, which is what I think you're saying. I think this is just snubbing their opponents' label. (cf jfm)
Many groups take up the word "science" as a PR move. I suspect that it is sometimes (in particular in anthropology) also a bit of "dark side epistemology" or at least to help them act more indignant. (cf Jayson)
After following this a bit more, and looking at some of the mailing list threads behind the scenes (threads in reaction to the change, not leading up to the change), it's pretty clear that what's going on on both sides is group identity signaling. The "pro-science" side is not really any more committed to empirical evidence or analytical rigor than the other (which I'd loosely identify as postmodernist).
The American Anthropological Association has apparently decided to ditch the word "science", arguably so they can promote political messages without hindrance from empirical data.
If so, this might be an example of dark side epistemology.
(Articles in Psychology Today and NYT).