How is that any different than adding a password? He's protecting his own interests so he won't be fired without a chance to come back to his job and finish automating the whole company. He made himself indispensable with the password. This would be another way to do it in case they figure out the password with some other methods, such as a keylogger, before letting him go.
There's a difference between protecting a buggy alpha, which he probably didn't realize (or maybe wouldn't be) company property, and intentionally making an artificially weaker program in order to ensure your job security.
