A user unfriendly app I know of that can do the job is a good old hex editor; can't think of a user friendly one though,
I too would love to know if anyone knows of a user friendly app that can do this.
Come to think of it, I believe WinISO (a user friendly app) lets you rename, delete, and possibly add files into the filesystem of an ISO. However, as you can see, its filesystem editing features are limited.
If no one else can help, perhaps you can propose your idea to the author of CDmage, IsoBuster, or even WinISO.