I don't know about it being rude, there's been tons of times for me when "calm down" has been fairly legitimate advice. There are many emotional states that aren't really conducive to reasoning and actions taken in those states can be regretable. Y'know, stuff like "calm down before you call your ex/quit your job/punch that person who insists on having a loud conversation on his or her cell phone right next to you in the computer lab, even though there is a 'no cell phones' sign right there."

I mean, I can see the merit in avoiding it in this community, but I don't think the phrase itself should be condemned.