I have looked through Channels and it doesn't seem like it is currently possible to exclude channels from the guide except for hiding them in each source.
I was hoping a feature might be possible in the future to create a Channel Collection (ideally using the Automatic Channels feature) to exclude other channel collections or some other group of channels. If that feature existed I could start a new Channel Collection with all channels from all of my sources but then exclude other channel collections I have made and don't want included (such as excluding all Sports channels I have organized, or all Spanish channels). I have a lot of channels so I feel like this would be easier and more dynamic rather than just manually selecting each channel that should be included as part of a Channel Collection.