Good point, you are probably right about the normal reaction from Joe Sixpack. But do you think Adult Swim would consider the risk/reward of an ad campaign and say "That 2 percent is enough for us," and do it anyway? Assuming they hadn't considered the possible reaction of the city authorities (which they obviously didn't).
Adult Swim fans are going to see the movie anyway, but I can't see that being even close to enough for a decent box office gross. The Aqua Teens are meant for a niche audience, and Cartoon Network is just being foolish if they have delusions of mass appeal.
That said, it makes sense for them to make some sort of an awareness grab toward the mainstream -- this wasn't the smartest way to go about it, though. Billboards and 30-second TV spots don't turn up on the front page of any newspapers or news sites, but they also don't create lawsuits and (even mistakenly) equate your brand with terrorism.
However, if they wanted to generate a buzz, I think they've got their wish. It remains to be seen if that buzz's negative undertone hurts Adult Swim, however.