To delete the channels, you simply uninstall them with WAD Manager.
Place the WADs of Configurable USB Loader and NeoGamma on your SD Card and open WAD Manager with IOS249 and disabled NAND emulation.
(The Configurable USB Loader channel is most likely not working because you don't have the application itself on your SD Card)
The LoadMii channel included in mauifrog's guide is for safety reasons.
You don't need it to run WAD Manager, but it'll be of help if you ever manage to update your Wii.