This all depends on the vehicle. For example, Toyota's Hybrid Synergy Drive (formerly Toyota Hybrid System) in their hybrids is entirely drive-by-wire, meaning there is no direct attachment between the steering column and pedals and the mechanics they control.
I see no reason why the ability to brake in my Prius couldn't be disabled by sabotaging the ECU, same with steering and acceleration. There's not a traditional transmission either, so I can't just force it into neutral and roll up a hill to stop. There's technically a mechanical linkage in the break pedal to the disc brakes should the ECU fail, but ECU failure and ECU tampering are two separate concerns.
With that said, I'm not overly concerned about electronic attacks on my vehicle at the moment, someone would still need to forcibly enter the cabin, connect to the OBDII port and make modifications to the ECU firmware, not something some jerk could do while we are going down the freeway. I would certainly feel a lot safer if the code running on the ECU was available for the community at large to dissect and inspect, though.