Just to chime in and give my unasked for $0.02 as someone who works in this field,
Mutinies are totally possible with big crews. Petropavlovsk, Chilean Navy, Brazilian Navy, Spithead and Nore, Invergordon, I could go on. Sometimes the whole crew is on board, sometimes it isn't. Officers and mutiny leaders will probably spend some time before the "big event" trying to make crew changes, putting sympathetic crew on board and loyalists off the boat.
You can usually function a big ship without all of its crew. Just to run the basics of a modern warship, you can probably lose, oh I dunno, up to half before you lose critical functions. You may not have a galley or a forward gunnery department or your first lieutenant division, but you can zoom and scoot to where you need to go. I'm sure that Overlords are even better built than this, but I would bet money I could take forty guys who know what they're doing and get turbines going from cold steel and at the very least, get underway with some random DDG.
I don't know of any systems that exist to halt ship mutinies except through personnel. Having good, well-trained, loyal officers and chiefs and sailors is enough to do the job in almost all cases. However, a strong imminent motivation i.e. "oh shoot we saw Nomads in LN" (and I don't know what this particular defection case is) might certainly get a lot of sailors on the mutiny gang.
Having a "remote control" for critical ship systems to be manipulated from some command center sounds like a horrendous design choice. Imagine if that system was accessed or hijacked by electronic warfare / intel forces of a hostile navy and suddenly they can cut your engines in the middle of battle! Or, Rheinland marines bumrush your headquarters and disable half the fleet. I definitely do not advise any navies building remote kill-switches for any system into their warships.
