You could create a program that you use as a template that does not include an email, since that is the different piece for each program. This way you won't have to remove the old email.
I'd still like to understand why you cannot unapprove this email. Is it saying that it is being referenced somewhere that it is not?
The general idea with cloning is that you re-use all the assets and use tokens to change out the content. While i understand this may not always be the case, I think creating a program template that you clone from each time will work for you.