Shisui's KA was the only other answer. But then Danzo ruined that. :/
-Itachi could not have used KA on his father with the eye Shisui gave him at that moment, because it was still on cooldown. Meaning that Shisui had used KA in that eye beforehand for something else. So that was out of the question.
-Telling Hiruzen about Danzo taking Shisui's eye wouldn't have made him lose his position. Danzo has done worse things and he has accepted them. That would just make things worse because then Danzo would know that Itachi would be the one with Shisui's other eye.
-If an Uchiha killed Danzo (Itachi could have at the time), then it would make the Uchiha look even worse and cause even more tension in the village. This is out of the question as well.
Hiruzen just shouldn't have let Danzo do whatever he wanted.