To be more precise, it would be a problem if GitHub got an Extended Validation certificate with the organization field containing the name of the domain owner rather than GitHub itself.
It would in fact be perfectly fine for a CA to issue an EV certificate containing "GitHub, Inc." and a domain that GitHub does not actually own, but which they control because someone pointed their A or CNAME record to GitHub pages. The Extended Validation Guidelines[1] do not require domain ownership for the organization requesting the certificate, it's enough to control it in a way that allows you to complete one of the blessed validation mechanisms defined in the Baseline Requirements.
[1]: https://cabforum-travis-artifacts.s3-us-west-2.amazonaws.com...
