Maybe it's a good idea to make it possible to enable both the Bookmarks view and the Tree view and that they would be placed beside each other. I manupulated two screenshots to give you an impression of what I mean: http://img62.imageshack.us/img62/3894/thunarrm0.png
Screenshot already shows the problem: A simple, easy to use thing will be turned into a Konqueror-like usability-problem. Aside that, somebody posted a patch for tree+shortcuts pane on thunar-dev a few days ago. I suggest you search the ML archives and grab the patch.
Please see https://bugzilla.xfce.org/show_bug.cgi?id=13449