If you disallow publication of GitHub Pages sites, any sites that are already published will remain published. You can manually unpublish the site. For more information, see Unpublishing a GitHub Pages site.
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In the upper-right corner of GitHub, click your profile picture, then click Organizations. 
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Next to the organization, click Settings. 
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In the "Access" section of the sidebar, click Member privileges. 
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Under "Pages creation", select or deselect Allow members to publish sites. 
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Click Save.