I have successfully tested basic DroneKit scripts on a companion computer (Raspberry Pi) to achieve autonomous flight on Pixhawk controlled 3DR ArduCopter. The RPi is also connected to various sensors, and crunches that data in real time in the same python script- to influence the flight. 
Is it possible to pilot the drone manually with a Taranis as usual, while RPi (with DroneKit running) remains connected to Pixhawk and overrides the radio when needed? For example, a background prevention mechanism that takes control and moves the copter away if the pilot is about to crash into a wall (which is easily sensed using a LIDAR).
Thank you!
While your vehicle is in any mode other than GUIDED, your dronekit script will not be able to control behaviour. However, the script can change the mode of the copter to GUIDED, send some commands, and then set the mode back to the previous mode when it is done.
The example you gave of using lidar for obstacle avoidance is already a feature in progress, being built directly into normal flight modes. Perhaps it's not documented well enough yet, but maybe try digging into the code to see how it works.
Is it possible to control Pixhawk quadcopter with a Taranis and a DroneKit script simultaneously?