"single, well-protected server"
It doesn't sound like it. Even our production servers hosted by a "rackspace" company have outgoing ports closed by default, we earn a tiny amount compared to RSA.
I know there will be reasons but honestly, the server should have been air-gapped or something. I can't imagine they need changing very often so why not copy it across the gap on a USB stick when you need it and leave it non-networked otherwise?
Of course, I know nothing about this organisation, it just sounds weird that a system that was so crucial was so vulnerable.