The arm almost certainly has a control system that can resolve that. Since humans suck at higher order control, the arm almost certainly has a control system that takes the operator's desired output (which will be a series of joint angles), and converts into the required motor torques. In this process, the control system almost certainly also does sanity checks to prevent self-intersections, collision with the space station, overtorqeuing the motors, and etc.
Replacing the human with a computer program therefore likely doesn't literally involve verifying that it will not karate chop the station - lower level control will take care of that for you.
However, as anyone who has worked with robot manipulators before, actually getting good performance out of them in variable environments (ie, not a controlled factory assembly line) is quite a bit of work - work that probably isn't worth it.
Replacing the human with a computer program therefore likely doesn't literally involve verifying that it will not karate chop the station - lower level control will take care of that for you.
However, as anyone who has worked with robot manipulators before, actually getting good performance out of them in variable environments (ie, not a controlled factory assembly line) is quite a bit of work - work that probably isn't worth it.