The Konqueror window is probably not being opened by KDE, since KDE 3.4 didn't have the ability to respond to a drive being inserted on its own. More likely, you're running ivman. If that's the case, then I recommend just uninstalling it, since KDE 3.5 has its own volume manager now.
As for changing the action for desktop icons, I've been trying to do the same sort of thing to make the icons work with automount. You can sorta kinda do that by modifying file associations. Just modify the file association for the media/removable* MIME types to use an appropriate command. The media:/whatever URI will be passed to this command, so you'll probably want to use a little script to convert this into the appropriate local path.
The problem I've found with this method is that it doesn't really work correctly when you double-click the icon. It seems to work right the first time, but after that it goes back to using the media:/ paths. However the open item on the context menu works as expected. It's really weird.