Who's to say the only reason he used Izanagi was to prepare for the other eye? He's not supposse to have it, so what better way to get rid of it then making it blind?Danzo had to use Izanagi to escape a simple Genjutsu from Shisui...
Also, if it wasn't for the surprise factor, Shisui would have been the one to rape him.
Even if we put Izanagi aside, the surprise factor still stays there. Shisui had no idea of Danzo having a Sharingan, nor did he know that there were root members around, preparing to catch him.Who's to say the only reason he used Izanagi was to prepare for the other eye? He's not supposse to have it, so what better way to get rid of it then making it blind?