How hard would it be to make this a RC feature? "Checkbox: when replying in this folder, file the sent message here".
look at plugin saveinsamefolder from myroundcube (http://code.google.com/p/myroundcube/)
you can not configure per folder but if you want the functionality for all folders it works well.
List info: http://lists.roundcube.net/users/ BT/9b404e9e