Hijacking the facts
Now that it's been officially declared to be unlawful interference, you'd have to take a contrarian view in questioning this paranoid conclusion - via the other possibilities.
Simply assuming that "somebody" was switching off comms equipment is to disregard a more simplistic explanation - such as an avionics bay/ main load centre explosion/fire that progressively disabled systems. A progressive failure that was epicentric to aircraft electrical (and thus also avionics) system integrity could conceivably knock out comms, transponders, ACARS etc and distract the pilots (getting on oxy, getting their oxy mask mikes to work, talking to the rear).
So after such an event, assuming the aircraft remained controllable, what would the pilots have left? Radio comms? Transponder? Flight instruments for control on a dark night? If there was a discernible horizon but despite cloud cover below to hide any land-mass, it may well have been controllable - however directionality might have been a problem (did they have an E2A wet compass?). So if they turned back towards KL in an essentially electrically inert airframe, it may have been a rough guess heading based on a timed turn and nothing by way of electronic navigation.
What might have happened in regard to height keeping? Was their altimeter disabled? Would that have led to a purported momentary excursion to 45,000 ft? If a 777 aircraft is partially electrically inert, what happens in respect of maintaining cabin altitude? Would the pilots be (or become) aware of any insidious depressurization? How long would their oxygen last? Would they be facing inevitable loss of consciousness if they'd remained at height - leading to the aircraft droning on westward (on autopilot or not). Could the pilots have become disabled leading to a Helios type scenario with a 3rd party (pax or rear-end crew) using the code to access the cockpit and trying to operate the aircraft?
Alternatively, although the cockpit door can prevent terrorist ingress, maybe the terrorist network became aware that they could access the avionics bay from the forward galley - and thus disable the aircraft from there via covertly disrupting comms and avionics (and cabin pressurization?) in an orderly sequence. One of their first tasks may have been to kill the cockpit to rear internal comms, thus leaving the pilots to wonder "What in hell is happening here?" -as various systems warnings cooked off).
After any such nasty terrorist disruptions in the avionics bay, the pilots would be left in a similar scenario to that described above, i.e. "flying by the seat of the pants on a dark and moonless night over-ocean". It would be challenging to say the least, even in daylight.
I doubt that all possibilities have thus far been credibly canvassed. The various data-points thus far established may be explicable via the technical intricacies encompassed within either of the above scenarios.
I'd like to hear any contrary views.