Really? I thought he was more a cloak and dagger kind of guy. This is a series about ninjas, and we know how they make their living.
BELIEVE IT!
Danzo gives his reason in the filler before taking the eye. Genjutsuing Fugaku isn't a permanent solution, and what if the rest of the clan turn against Fugaku and try to carry out the coup anyway? Or, what if Shisui is discovered. Sharingan/Byakugan/Rinnegan can all see chakra flow and detect when a person is under genjutsu. It's the victim of KA them self, who will never be aware. Lastly, how long until Shisui or someone else decides to use Shisui's eye power against Danzo, Hiruzen or the Leaf?
A nasty business. But one that Danzo, Homura, Koharu and Hiruzen felt they could live with. Remember, clans in the NV (Yuki, Kaguya, Uzumaki, Senju) disappear or are wiped out all the time. And no one bats an eyelash.