From Rockstar, via, http://www.pro-g.co.uk/news/nid/88/1073/
"So far we have learned that the "hot coffee" modification is the work of a determined group of hackers who have gone to significant trouble to alter scenes in the official version of the game," reads the statement. "In violation of the software user agreement, hackers created the 'hot coffee' modification by disassembling and then combining, recompiling and altering the game's source code. Since the 'hot coffee' scenes cannot be created without intentional and significant technical modifications and reverse engineering of the game's source code, we are currently investigating ways that we can increase the security protection of the source code and prevent the game from being altered by the 'hot coffee' modification."
The statement does still leave the door open as to whether or not the code was originally on the disc or not. It seems to say that the hackers significantly altered scenes which were already there. There's a lot of gray area for investigators. The investigation by the ESRB continues and we'll update you on any happenings.