I would make a new module and put a on_key_press() function inside it, without the line that blocks keypresses while the game is paused. In my opinion this would be the most non-confusing way of doing this. Actually I just made one. Just import this module into AGS from the Module Manager.
http://koti.mbnet.fi/pabsoft/ags/keypress_module.scm
There.
http://koti.mbnet.fi/pabsoft/ags/keypress_module.scm
There.