I wouldn't recommend stopping the repository via the QMC. Stop ALL QlikSense services (including the RepositoryDatabase) via the server it lives on and upgrade there. Then when complete, reboot the server and all your services should start back up automatically.
Also, don't forget to backup the C:\ProgramData\Qlik\Sense and C:\Program Files\Qlik\Sense locations after you stop the processes and before the upgrade.
Hi Louise - You can try to login to the QMC using the service account you are using to run the Qlik services under (Granted you have access to this account). That account should have all the access it needs.
As Jason mentioned in his reply, you should stop the QS services from the 'Services' utility within the Windows Server.