If you open IE's Preferences and go the to "Received Files" area, under "Helper Application", you should get a list of file identifications by MIME type (e.g. "application/stuffit") and suffix (e.g. ".sit") Scroll down the list and select the .sit and stuffit types that are set to open with Stuffit Expander, and delete them. (Maybe use "Edit" first make a note of the settings first, in case you ever change your mind and want to put them back.)
(I checked that on OS X's IE 5.2, OS 9's IE may have slightly different terms for those Preference pane titles, but the principle of the Help App binding by suffix and MIME type is the same.)