I don't know if someone has already suggested a secure way to distribute the SSL certificates, but I think the way to do it is to have several people running control terminals that have the certs securely stored, and then propagating them to secured memory through SSH connections. The users get email notifications telling them when a server has restarted, and they then need to run a script that securely loads the certs into memory on the server.

I in fact have had a somewhat similar quandry with running a simple server box (in this case, my laptop) and I made scripts on my main workstation that push shell commands to perform storage unlocks. I think this probably would be the way to do it on these servers. Store the certificates on a secure partition, and have it automatically unmount when the server restarts, and require manual unlock to re-enable it. Since you have a cluster running, yes this requires some attention, but with sufficient, geographically distributed administrators (trusted, of course) they can fire off an SSH command to unlock the certificate stores and keep the secure storage from being unlockable from the server.

I of course am no expert on this but I puzzled through this problem for my own specific application. My goal was that it would be impossible to physically compromise the security of my secure storage partition, because I was physically monitoring and ensuring the controlling system was secure.