There is no "turning off" zones. If an area is included in a given scenario that's it.
Er, well, they are turned over to computer control, although i've never done that and don't recommend it... (bad, bad things can and usually do happen).
You can play some of the "limited" scenarios that don't involve the whole "board"... or, you could attempt a mod... much work involved there.
Lastly, to speed things up, you can alter the time settings in your "preferences"... also, if you are playing against the AI, you can hit "escape", and that will speed up the replay (but supposedly might result in a "Replay Bug" if you are the Japanese playing the non-AI Allies.)