Eu faria assim:
Host project_1
HostName github.com
IdentityFile /etc/ssh/my_project_1_github_deploy_key
Host project_2
HostName github.com
IdentityFile /etc/ssh/my_project_2_github_deploy_key
e, em seguida, use project_1 ou project_2 como host para acessar o repositório.