Yes, Danzo did use Izanagi on Shisui, and people seem to have a problem with that. But if Shisui had wasted his KA on Danzo, I bet that no one would be batting an eyelash.
The fact of the matter is that Danzo didn't want to kill Shisui, he wanted his eye and succeeded, while Shisui didn't want to kill Danzo considering that it would make the Konoha/Uchiha situation worse. They were even in this respect.
It is Shisui's fault that this happened, considering that he completely let his guard down, and then proceeded to tell Danzo exactly how long it would take to be released from that 3-tomoe genjutsu. Which was essentially pointless, considering that Danzo would know when he'd be released and if it's only a few minutes, there wouldn't be anything to be worried about. If Shisui were smart, he would have bolted out of there when he had the chance, however, he did not and it just looks bad on his part.
Not denying that Shisui is a powerful ninja, but that really wasn't a smart decision on his part. You can have alot of power in this series, but if you're not smart about it then it won't matter in the end. If you put someone else with a sharingan in Shisui's place, like Itachi or Kakashi...would they let their guard down? No, probably not. Itachi would probably put Danzo under a genjutsu and then leave. Kakashi and Itachi also seem to always have their guard up in this arc.
Either way, no matter how much you dislike Danzo, you cannot deny that he fodderized Shisui with only one arm and that the backup wasn't needed, considering that the incident occurred right before they arrived.