So to my understanding of the situation Manji was hit with a technique, and then activated Izanagi to avoid the technique.
However it is also to my understanding that Izanagi had to be active before the receiving the attack, such as in Danzo's case, the izanagi had already been activated whenever he was pierced with the arrow, which allowed him to survive the attack.
HOWEVER; on the other hand. It's also to my understanding that Manji's survival was discussed and agreed upon by himself and Kirk, to my knowledge there was no judge for the situation so the decision that was made between the two of them would have been final, wouldn't it?
I might be misunderstanding the situation though, I was directly apart of it so I mean yeah. But what i'm trying to say is if the two of them agreed that Manji would survive the attack, As kirk was the deliverer, and Manji was the receiver, then it would be decided that he wasn't dead right? Just like in my stupidly embarrassing situation with Hazama awhile back, he and I agreed that I wasn't dead, and continued on our days (we're good buds now <3).
But I mean that's just my opinion on the situation, if i'm wrong about any of my details don't shoot the messenger, It's just how I was lead to believe the situation played out, if i'm wrong please correct meh.