It sounds like the Transponder was manually shut off (a switch on the center console). It's much more difficult to shut the ACARS down. It doesn't have an on off switch. The circuit breaker could be pulled, but it sounds like that did not happen. That's why the ACARS was still pinging the IMARSAT. Finding the correct circuit breaker on the overhead panel would be time consuming, unless one knew exactly which circuit breakers to pull before hand.
Even for the pilots, it would be difficult to know how to shut all the communications down. There is a lot of automatic stuff (like the engine data) that is transmitted. The plane also automatically changes what antenna the data is transmitted through. Over land the ACARS transmits on VHF frequency. It automatically switches to the Satellite antenna when the plan leaves VHF range. Anyone knowledgeable enough to alter that would have to have been trained on the 777.