Peter: The passenger sat phone system can be disabled in seconds from the flight deck and block all calls. I would be very surprised if , having found out how to disable ACARS, "they" didn't also disable the phones.
I am still mystified by this theory that ACARS reports all waypoints as you pass over. It doesn't. If you are logged on to ADS then the aircraft usually reports it's position over every waypoint, and then every 18 mins if running a standard "contract" with ATC. The aircraft would not report every waypoint as a matter of course.
As for cellphones, you are hard pushed to get ANY service above about 2000' unless in remote areas (Afghanistan, some parts of Russia, Africa) where you have 60k mast spacing and your phone isn't logged onto multiple masts simultaneously. Even then your phone will only hold a connection for a matter of 2-3 minutes max.