I really don't see the problem. Once you set your cname record to GitHub, you've essentially yielded all control to them.
If you don't like that, don't set a cname record.
If you don't like that, don't set a cname record.
"GitHub Pages sites have been issued SSL certificates from Let's Encrypt, enabling HTTPS for your custom domain. This isn't officially supported yet and it's not possible for you to enable and enforce it on your sites at this time."
EDIT: found out the "official statement" here https://gist.github.com/coolaj86/e07d42f5961c68fc1fc8#gistco...
Fortunately LE are moving towards shorter and shorter validity periods for certs, which at least limits your risk somewhat.