Hello @Nightly, welcome to the community!
Repositories can be linked to a site on Netlify, which can in turn be linked to a domain. As a site cannot exist without a repository to pull from, the entire site should be deleted. Alternately you can go to github and remove Netlify as an “Authorized App” which will prevent Netlify from accessing your GitHub repositories in the future.
To disassociate a domain name with a site, visit the site dashboard, select the site you want to edit, and then click “settings”.
Then select “Domain Management” from the menu on the left side. You’ll see a list of domains associated with the site. To remove one, click the “Options” dropdown next to the domain you want to disassociate, and then click “Remove Domain”. Note that this does not delete your domain name, only the link created between it and your site.