Like many others, I've seen the facepalm used to represent a fairly broad spectrum of emotions, both directed at one's own actions and that of others. It's certainly been around since well before Star Trek, since I remember it being used before that show was on TV, and in fact I wouldn't be surprised if William Shatner brought it with him as part of his Canadian heritage; it's endemic here, and has been for generations.
I've taken a look at a lot of the examples that were provided of "uncivil" use of the facepalm template. Careful backtracking of several of the discussions revealed that the template doesn't seem to be being used with "newbie" editors as frequently as was being put forward; in fact, it seemed to be used most frequently when dealing with editors to whom explanations of poilcy/guideline had already been given, sometimes by multiple users. One example in particular hit home to me because it was in response to a multi-project serial sockmaster on his fourth or fifth account, "improving" an article with his own personal version of history that conveniently also bolstered his financial prospects.
So perhaps a better focus of discussion would be "how to deal with editors who are unable to or unwilling to understand project guidelines and policies". It seems that the primary use of this template is by editors expressing frustration at the inability, despite their best efforts, to address this issue.
Risker/Anne