Which is why Valve wont be doing anything about it. VAC only covers multiplayer games. They couldn't give any less of a shit whether or not you mod your single player games. Hell, they pretty much support it. (Steam Workshop)loa said:
As for patching the game to not allow this, I really don't think there is much Ubisoft can do that would be effective in the long term other than directly altering the .exe file for the game to remove those specific segments, which I doubt they would do since it would only provide for a longer delay before the content is modded in again. I don't really think it's worth even trying.