We had one of out github enterprise organization owners leave the company recently and he did not transfer ownership to any of the other admins. Is there anyway to change an organization owner as a site admin or will we be forced to migrate all of the repos to a new Organization?
Yes, there is but , assuming you are unable to assume the id of the person who left because they are suspended, it requires access to the admin shell.
ghe-org-admin-promote will make any github admin an admin of the org . If you dont give a user it will add ALL the github admins, which probably is not what you want to do. (since you have to be admin on the shell, it doesn't know what your github user is by default)