You can use multiple deploy keys for Github created with ssh-keygen following with these steps.

You have to add to your ~/.ssh/config

Host github_deploy_key_1
    Hostname github.com
    User git
    IdentityFile ~/.ssh/github_deploy_key_1_rsa

Host github_deploy_key_2
    Hostname github.com
    User git
    IdentityFile ~/.ssh/github_deploy_key_2_rsa

If you haven’t added your github name on git:

git config --global user.name "yourgithubname"
git config --global user.email "youremail@example.com"

Then clone your repository specifying your custom host, adapting what github suggest to you on repo page:

git clone git@github_deploy_key_1:yourgithubname/your-repo.git

If you have enabled push permissions you can use this deploy key even to update the repository.

In this way you can keep a server clean from your github passepartout and add only the keys it needs.