[tracker1]

You could always use CloudFlare directly for that... I would presume that their underlying connection to Github is very close and reliable in terms of risk for MITM.

[kirushik]

Even better, you could CNAME your custom domain into the *.github.io domain, which is protected by a wildcard https.

So you traffic between CloudFlare and GitHub will also be secured.

[holic]

Last I checked, this doesn't actually work with the way *.github.io is set up.