I'm on the same situation, NKit can't convert the CISO back to ISO, not even after updating the No-Intro DAT, so NKit won't delete the resulting file, but allow me to shed some light on this matter:
Followed most recommendations on this thread to convert the CISO into an ISO, which came up as a full Wii backup filesize file (more than 4 GB), useless in any way, not recognized by any known software commonly used to deal with Wii or NGC backups.
Then a glimpse of genius came to me, if the CISO is a compressed ISO, 7Zip must be my saviour. So I opened the CISO using 7Zip and extracted it into a folder, and it worked!
It came up as a folder structure with some DOL files and a very rare BIN inside a [BOOT] folder. The main DOL file can be opened using Dolphin and the game will run perfectly. So then, the same DOL file should be useable on a Wii console using a backup loader of some sort (haven't tried).
Now I'm trying to find a way to convert the folder structure into a valid NGC ISO file, GC Rebuilder didn't work though, creating an ISO from the folder didn't worked, so this last step is the one I'm missing to get a NGC ISO that I can try playing on my real Wii.
If someone can help me on this, thanks in advance.