"Hurt" is not quite the right word. "Hurt" seems related to "suffering" which the essay is attempting to separate from "pain".

New information is going to reconfigure your thinking to some degree. Like scarring your muscles through exercise you can get used to the feeling of your thoughts being reconfigured.

If you watch young children learn anything, you will see that process of reconfiguration happen before your eyes. The pain involved in that experience may not be particularly hurtful (though sometimes it is).