Seems the Rockstar vs. EA and The Simpson's game fiasco didn't hold as much truth as you would think, it was mostly over-blown. EA rep Tammy Schachter stated to Kotaku:

Thanks for giving me the opportunity to put these rumors to rest. There was absolutely no content removed from the game as a result of complaints or comments by another publisher.

The spoof content and parody storyline for The Simpsons Game has been in place since the early stages of the titles' development. In-game spoof content for Grand Theft Scratchy has not been removed.

Information is sketchy at the moment, but it sounds as if Rockstar were offering there opinion on the game, saying most likely they thought it was wrong to be using "Grand Theft ______" for a mission name and that was taken by the press in the usual way, the wrong way. Which has spiked all this and caused fueds, where as nothing was really going on. Turns out the level has not changed, the content and all referenced to "Grand Theft Scratchy" are still in the game, and the level name was never actually changed either. Rockstar deserve an appology I think, as usual they are the bad guys in the media's eyes...