The problem was that Rockstar hid the source code for the Hot Coffee Mod in the game. Then someone found out and thanks to the internet, it spread like wildfire on a hot day. Eventually, it was rendered playable and that's when Rockstar got into hot water.
It's not just because they had that in the game that got San Andreas busted. It's because they hid it in the game, never acknowledged it and when it was discovered, they denied having putting it in the game despite the hard evidence showing it was embedded within the core programming of the game. It was only after a while they coughed up the truth.
By then, it was too late to simply patch it up. They already threw the whole damn tank of gas in the fire.
EDIT! Manhunt 2 has been put on "temporary suspension" by Take-Two Interactive.