As a Fundamentalist, and therefore presumably among the prime targets of that particular comment, let me say, (a) As a joke, it's not very funny. It's really more "ridicule" or "random insult" than "joke". And (b) I vote to let it stand. Such a trivial insult is not going to send me running to the corner, sobbing hysterically.
(Indeed, I'm happy to see such lame insults from my opponents. Let us Fundamentalists present carefully reasoned historical, philosophical, and scientific arguments, while the atheists shout, "You're a moron! Ha ha ha", and let's see who wins in the court of public debate. :-)
When someone tells an ethnic or religious or political or whatever joke that is actually funny, I think it can be entertaining, and help to break the tedium. But of course this forum isn't a place for protracted comedy routines, nor for political/social/religious debate.
In my humble opinion, an occasional good-natured joke is a positive thing that helps keep a dry subject entertaining. Of course, while much humor hinges on making fun of the foibles of people, there is a point where it becomes deliberately insulting. Like, a joke whose humor relies on the fact that a certain ethnic group has different tastes in music or has its own dialect should be harmless; a joke that relies for its humor on the assumption that a certain ethnic group are lazy or stupid or criminals is likely just insulting. Saying, "Isn't it funny how your political party and mine see this differently" can make for a good joke. Saying, "Isn't it funny how your political party is too stupid to understand this obvious reality" is an insult.
Are there gray areas? Sure. For a stand-up comic, pushing the gray areas may make for edgy comedy. But for a forum like this, it's just not appropriate.
Oh, and by the way, if it would be an outrageous insult for somebody to say this about you, that it's an outrageous insult for you to say it about someone else. I don't know how often I've heard the defense, "But those people ARE stupid, so they have no right to complain when we make jokes about them, but my group are intelligent, so if you say such a thing about us you're just out of line." Insults do not cease to be insults because they are true. Besides, if you don't see the obvious bias in your high opinions of yourself compared to others ... well, that's a subject for jokes right there.
My conclusion: A little humor now and then is a good thing. But on a forum like this, err on the side of being unoffensive.