I see what you're getting at, and the more I think about it, I agree with whoever said it... it isn't so much the joke, as the musical sting and Pepe's overreaction to it that really made it unsettling. It really seems like something off the cuff that really wouldn't have made it into the final cut. Like they were just messing around trying to make the funniest of a decidedly bad script. The fact that they left it in there as a jaded attempt to be adult (trying TOO hard to do the same stuff that actually worked in VMX, but fell flat here).
Of course, I thought the joke was REALLY funny initially when it was shown briefly as a clip on AFV... but in the context of the movie, it just seemed... well, like it came at the wrong time to make that joke.
We could turn this into a "Why MupOz sucks" thread, but I really think it had an unsettling look throughout. Alkmost like someone was trying to be Tim Burton-esque and 1960's Batman at the same time, and it just made the movie look dark, sinister, and forced... even the bright sunny parts felt unsettling.