I think the short answer is probably, nobody at Github has a lot of macro-level regrets at this point.
I think the real issue is that the Rails community should be supremely grateful that they have a team like Github's building on the framework they've chosen. They all get to draft off the deployment/security/development/reliability work Github sinks into the platform.
And, painful though it will surely be for HN to hear this, snags like the one today are how frameworks eventually get to be solid. Spent much time looking at Java Spring's track record?