Looking at CF's help again and having used them a bit, there seems to be no way at all to enable full encryption (user-CF-github) with CF's non-enterprise offerings. This is because the request from CF to Github is still requested with your domain name (TLS and host header).
In order for it to work with Github's *.github.io cert, Cloudflare would need to offer an option to rewrite the request itself, not just proxy it.