So even Fugaku had MS.....I wonder if he could have stopped Itachi if he tried.
Fugaku asked Itachi for help in this episode. He said himself that with both his and his son's MS they could conquer Konoha.
Itachi chose Village's site in this internal conflict and for him the hardest part was to defeat his father and he also said it won't be an easy job.
In the end, Fugaku did not fight his son because, as he said, he won't be fighting his son to death. I think that Itachi's decission was decisive in attempt to take authority over Konoha. By simple words - if Itachi joins, we can make it and if not - we are doomed. That's why at the end he said those words to his son.