You can't really do anything to avoid that. Favorites, History Items, etc will fill up the whole panel. The only thing you could do is add a remove button next to every entry (which would be really annoying).
nice work. but what about the tabs and the bookmarks bar? do they only show to the right of that panel? I think they should, like marlin. but will it still look good, specially the bookmark bar, with the handle between them?