Earlier quoted context omitted.
If someone compromised the key they also compromised the system used to automatically generate more keys, so a short expiration is not as helpful as it looks. It's even worse than that: A smart attacker will copy the method used to generate keys, and leave the server. Then they can keep generating keys and you will probably never notice. I feel that automation is a mistake, something security sensitive like this shou…
I'm not in the beta, and thus haven't been able to play with it yet. But, I don't believe there'd be anything prohibiting you from generating the certs on a separate machine. In fact, I'd imagine that's what you'd want to do (if you have more than one server) rather than generating a separate certificate for every web server or load balancer.
It would be trivial to move this to a separate machine by using a reverse proxy for .well-known instead of serving it directly from your load balancer's filesystem. The rest is just scp'ing your certificates and keys to your load balancers (or using your configuration management software of choice to achieve the same). With ACME being an open protocol it's quite likely that someone will end up writing a client specifically for this use-case, making it even easier.