I guess this would be a mod to the existing duplicate links checker, which is site (database) wide.
I am thinking when there may be an SQL solution to this, but it would be much better right out the links control panel.
I like the idea of site-wide fixes, which go through in one swoop, and remove all duplicate links which occur in any same category, taking the links which have a LinkOwner of 'admin' only, and leaving the user submitted ones. This is an especially useful function if you have editors adding links and you cannot check 30,000 categories manually.
Is this just useful to someone who has editors, or to anyone? I think if you have a site which lets users sumit without admin validation, this would also come in handy. It could go into our proposed editor plugin? Or into a housekeeping, or tools plugin