Make sure that the SSH keys are tightly restricted in the authorized_keys file so they can only run the commands that need to be run unattended. If possible, also restrict them by source IP address. Here's an example authorized_keys file that I have in production for doing unattended backups:
command="/usr/local/backups/backup_server /etc/snapshot_backup_list",no-port-forwarding,no-agent-forwarding,no-X11-forwarding,no-pty,from="10.70.0.0/16" ssh-rsa AAAAB...
I wouldn't worry unduly about protecting the keys themselves - since they need to be accessible for unattended operation, there's not much you can do to prevent them from being accessible to an intruder.