Thing is Itachi knew what Hashirama envisioned to unify all clans in the newly forged village and system he and Madara created. But discontent arises and ideals take root especially for the Uchiha. Itachi look beyond his clan, just like his best friend Shisui whom both carries the will of fire. Shisui dont want his ocular powers to fall to the Uchiha nor too Danzo instead he wanted Itachi to take it, that means something. I don't know why Fugaku as the clan head will just stop the his clan's coup de tat but maybe he's thinking even if he stepdown as clan head or silence the coup de tats nothing will really change, so he just accepted his death in his own son's hand this the annihilation of a clan. I think Fugaku knows that the coup de tat will weaken the Leaf, the Uchiha afterall have special abilities and can fight the military force of Konoha "many of whom are veterans if you look back" when after the war Minato was the 4th Kage Fugaku also became the Wicked Eye. Just imagine a civil war broke out in your country and your rival nations heard of it they will do anything to get the upper hand, during at that time Leaf was always the powerful village among the shinobi villages. Weakening the Leaf will always be in their favor. Itachi feared Leaf's utter destruction, and he was true adherer and loyal to the leaf.
