As far as injecting JS after server compromise: At that point, an equal concern is really attacker access to application memory, as we protect against the (admittedly edge) case where the attacker replaces the served Javascript but doesn't have access to memory. We've taken steps to reduce the opportunity for memory compromise.
Also, we are actually working on a reaction-oriented intrusion detection system that will take appropriate actions when invariants are tripped. But more importantly, we're moving to the daemon model, where customers have much more control over the security of their systems at the network level.
Many service providers, including DNS and hosting providers, use web-based control panels and must properly secure their systems. It's not a requirement that's unique to us. If you offer SaaS, you have to lock it down.