The newest version (0.4-beta) of my Comment E-Mail Verification plugin now has an option to hold comments for moderation even after the authors have verified their E-mail addresses.
Download it directly from the wordpress.org plugin directory
This update was inspired by user comments. Thanks for all your input.
This is a beta version because the entire moderation/verification process requires some more streamlining and new default messages, but I felt there would be an audience for an early update anyway. If you have any suggestions or spotted an error: please share!