Hmm, this is a good question, I "think" the easiest is to mount the .ssh folder form the host to the container itself. Then also mount clearml.conf into the container with force_git_ssh_protocol: true see here
https://github.com/allegroai/clearml-agent/blob/6c5087e425bcc9911c78751e2a6ae3e1c0640180/docs/clearml.conf#L25

btw: ssh credentials even though sound more secure are usually less (since they easily contain too broad credentials and other access rights), just my 2 cents 🙂 I would use user + access-token (which is the same as password only you can have multiple of those with limited access, see github personal access tokens https://docs.github.com/en/authentication/keeping-your-account-and-data-secure/creating-a-personal-access-token )