Recalling a (quite mediocre) novel I've read some time ago, a man-in-the-middle attack against the field bus *could* be imaginable.

While I don't know anything about field bus protocols used in aviation (and whether commands sent over the bus are signed or otherwise authenticated), I would probably not attack the avionics software (or the hardware it's running on).

The avionics systems themselves don't "fly" the aircraft, they only calculate commands that are used as inputs to servos, hydraulic valves and the like. What if someone (for example, a mole in engineering) plugs in some obscure device between the bus controller and the actuator (or replacing the bus controller for one or several actuators), manipulating the commands executed by the actuator?

This should be enough to render an aircraft uncontrollable by the pilots. Of course this is nothing that could be done by plugging an iDevice somewhere into the plane..