Depends. Is it a select field? If so, then you can disable an option. It will remain on issues where it has been used, and available for search, but no-one will be able to add it to an issue any more.
For other fields, there's no real "delete a value"
Thanks Nic. I guess I will have to get my JIRA version upgraded to display the "Disable" option.
I think it arrived in 4.3...
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