It depends on what you my by "doing it by hand." The update process is "automated" in the sense that it's completely scripted. Every step is known ahead of time, and has been extensively tested on ground-based duplicates of the flight hardware. The only aspect of the process that is done "by hand" is "pushing the big red button" to initiate the next step of the process, and even this is a very stylized and well rehearsed process. The only reason for having even this step of the process be manual is so that humans can assess the situation between steps and satisfy themselves that nothing has gone wrong with one step before proceeding to the next. That's the real challenge in a situation like this: your communications link is operating on the hairy edge of the limits imposed by the laws of physics, so lots of things can go wrong in production that worked in rehearsal.