From a morality standpoint, what is the difference between shutting it down and an indefinite state of stasis? The brain wouldn't know any different, it would just cease to process for a period of time, and then resume processing later. It would be just like a blackout. Except since the brain only receives stimulus from a simulated environment, the environment could be frozen as well.
So, if everything freezes and restarts at a later time, the brain would not perceive any missing time.
You're assuming isolation. No feedback. It wouldn't perceive any missing time if it had no contact with the outer world. I think that's treating the brain as if it was just a computer.
Ahh, that's an excellent point; for any of my argument to stand, it would definitely require full isolation (akin to what the current Blue Brain has right now).
So, if everything freezes and restarts at a later time, the brain would not perceive any missing time.