I just came up with an alternate solution that seems to work on my WP 3.0.3 install!
In /cms-tree-page-view/functions.php under "function cms_tpv_admin_menu()" I changed...
add_submenu_page($slug, $post_type_object->labels->name . " Tree View", $post_type_object->labels->name . " Tree View", "edit_pages", "cms-tpv-page-$one_menu_post_type", "cms_tpv_pages_page");
...to...
add_menu_page( $post_type_object->labels->name . " Tree View", $post_type_object->labels->name . " Tree View", "edit_pages", "cms-tpv-page-$one_menu_post_type", "cms_tpv_pages_page", '', 1 );
That moves the "Pages Tree View" menu item out from under "Pages" altogether.
Then I installed the "Admin Menu Editor" plugin. I then used Admin Menu Editor to hide the "Pages" and other unneeded top level menu items, as well as renamed "Pages Tree View" to "Add/Edit Pages" for user clarity. And SHAZAM! It woiks!!
Thus, it may actually be easier to incorporate this work-around in future versions by making your plugin a top-level menu item as listed above, then putting some code into your plugin to hide the "Pages" link. That way "Admin Menu Editor" would not be required for this to work.
I'd appreciate any feedback you may have. Thanks!