is there any way that you can get to the kopete main window? if so, there are 2 checkboxes in the "behaviour" tab of the "configure Kopete" menu item which are "show icon in system tray" and "start hidden" (or words to that effect).
if not, have a look in ~/.kde/share/config/kopeterc for the relevant options. you will need to restart kopete for changes made there to take effect