Copy the tracks of the selected iTunes Smart Playlist to their own segregated playlist on iPod. On subsequent runs, when the same iTunes Smart Playlist is selected, the corresponding iPod playlist will be deleted and then re-created. No tracks will be added to iPod's main library. Strangely, when tracks are copied this way (unlike with drag-and-drop or automatic updating), they do not populate iPod's main library, thus reducing the chance of disturbing tracks in other iPod playlists when they are deleted.
• Your iPod must be set to "manually manage songs and playlists".