There are a number of reasons you may want to uninstall a repo from a site, and you can do this easily through the platform.
Login and select the website from the server dashboard, and then slect FTPS, SSH & GIT
Scroll down the page to the Deployment section and beneath Deployment History is the uninstall section. Click Uninstall.
You will be presented with 2 options; Yes, and clear out the /public directory or Yes, but leave the files in the /public directory. Select which option you want.
The repo will then be uninstalled and you will see a notification that it's been deautherised.