In our application we have two modes of vehicle operation: manual and autonomous. Meaning that when vehicle is operated autonomously we control a brushed DC-motor using an H-bridge. In manual mode we don't control it, DC motor will see high impedance on its leads and can be backdriven. So in manual mode we want as less resistance as possible to backdrive the motor and we want to protect our circuitry from charge generated by the motor and the motor itself. Is there a common practice for that?
Basically you need a diode in series with the supply to the motor -- that will prevent the motor from supplying power back to the supply.
Trouble is the diode will drop 0.7 V and will dissipate power -- you can use a MOSFET in the supply or GND connection and drive it on when the motor is on, and off when the motor is off. You'll have to connect that FET with drain & source backwards from normal usage.
All you need to do to transition from automatic into manual is disconnect the motor from the H-bridge using switches or relays. The switches will provide electrical isolation from the motor, preventing circuit damage. Having the motor 'open-circuit' will minimise the torque required to turn the motor shaft.