That's erroneous. The Iron Throne is the highest in hierarchy, everyone in Westeros down to the peasants answer to the Iron Throne first. If Joffrey were to kill his Grandfather, he'd just have to replace him with another Warden of the West. If anyone got butthurt and become disloyal over him killing Tywin, they're automatically rebels and traitors.
Actually the only reason Joffrey didn't get the boot from the Iron Throne to begin with is because he had Tywin's backing...all of the Baratheon bannermen threw their support behind Renly and/or Stannis, while the Northmen fell in with Robb.
Joffrey killing Tywin would just create more chaos because there is no guarantee that the Lannister bannermen would decide to fall in line behind Joffrey. the little psychopath has no support without his grandfather (and his grandfather's money).