I agree with the concept that when the leadership orders you to commit evil being a soldier and saying I follow the chain of command does not absolve you of blame. Also if you think about it, it was quite selfish of Itachi to murder every Uchiha man, woman and child but leave the one he loved alone. In the series this is shown as his love but in reality it was a flaw in his thinking; what made Sasuke's life more valuable than that of another Uchiha child?

On this basis I think you can say that Itachi should not have become Hokage as he has a proven track record of letting his personal interests override the mission at hand and also to execute immoral missions. But then this claim can also be leveled at Sandaime for letting Orochimaru go and also allowing the Uchiha massacre to go ahead.

I think we are actually reaching the limits of the manga's capability to establish values which should guide governance and a nation with this discussion. On a simplistic level the actions of both Sandaime and Itachi are shown as acts of love but if taken in the greater context they are decisions which had massive consequences.