The Repository Viewer portlet should offer to remove entries that were formerly added by the user (that are not part of the server configuration itself).
If you can add repository entries via the console it would be consistent to remove them via the console, too.
On the details view for an entry there should be e.g.
|Assignee||David Jencks [ djencks ]|
|Status||Open [ 1 ]||Closed [ 6 ]|
|Resolution||Fixed [ 1 ]|