I think what you're describing is more a culture problem than an issue with the design of the FMS or pilots receiving incorrect information from instruments.
Any pilot will tell you the very last thing you want is to be at war with your own aircraft (or its instruments), but incorrect readings should not solely cause an incident. This is also the case with AF447. I'm more likely after reading the CVR to put the incident down to poor communication between the crew (in the industry known as CRM or Crew / Cockpit Resource Management) [1].
The crew failed to effectively communicate what each other were doing, to the extent where they were inputting opposite commands to the flight controls and had a misunderstanding of what conditions triggered certain flight control modes [2] of the Airbus' autopilot.
Coming back to the original point around culture and training, it was evident that the more junior pilots were relying on certain "protections" the autopilot has against conditions like a stall. It's this reliance upon a computer (commanding a full nose-up during a stall) and lack of understanding of how the aircraft's flight computer acts under certain conditions that ultimately ended 228 people's lives. The French investigation concluded that the inconsistency of speed measurements was only one of seven factors that caused the accident.
[1] http://en.wikipedia.org/wiki/Crew_Resource_Management
[2] http://en.wikipedia.org/wiki/Flight_control_modes_%28electro...
EDIT: Having said that, I would not want to be the pilot flying an aircraft where I can't trust my own instruments, however there are numerous cases (QF72 [3] comes to mind) where pilots have had to disregard most if not all digital instrument readings and stick to the bare minimum to safely land.
[3] http://en.wikipedia.org/wiki/Qantas_Flight_72