Given the lyrics it was pretty much ineviteble that the meme would "evolve" in this direction:
Harlem Shake (al qaeda edition) is a collection of clips of "terrorist-looking" people moving and dancing to the Harlem Shake song, but doesn't really follow the "rules" of the meme (unlike the other examples). I doubt that the scenes were originally filmed with the intention of making a 'Harlem shake video'.
Harlem Shake (Terrorist Version) and (Terrorist Version 2) seem to be from a Dominican comedy group and features a number of "terrorists" standing in a basement around a "hostage" tied up to a chair.
Harlem Shake (Al Qaeda) - or not features three "terrorists" out in the woods with three "captives" on their knees and I'd guess that it was put together by frat boys. Both of these last two examples are oddly homoerotic but it doesn't seem uncommon for the meme.