I do that all the time.
While you cannot literally delete the folder from SVN as though it had never been, you can do the next best thing.
1. Delete the folder in Eclipse. Do NOT use the command line or Windows explorer to do this, use the Eclipse navigator. It should decorate the folder icon with a red "X", indicating that deletion has been done. This will also schedule any child files and folders for deletion.
2. Commit that deletion to svn. That should make the folder vanish from the Navigator. For good measure, update the working copy FROM svn head after the commit in order to get everything in sync.
3. Manually create the folder using the Eclipse navigator "new folder" function.
4. Use the context menu to tag the new copy of the folder as "svn:ignore". Commit this new folder and again update the project.