This should not only be a global configuration option, but rather one that can be changed temporarily and programmatically by other modules that want to copy or convert content nodes and comments.
For example, if some module wants to convert a node to a different type, all comments need to be copied. This now triggers a comment notification for all users involved in a discussion that may be years old.
If there is a quick hack to prevent this, I'd like to know. Using some global Drupal variable should do the trick, I suppose.