I suggest 2 possible fixes:
1) Return the focus to the file browser pane after any mouse-based interaction with any of the Places applet. This means that one can quickly change between clicking in the Places pane and using keyboard based navigation in the main window. I specify "mouse-based interaction" as it should still be possible to tab to the side pane and interact with it with the keyboard. IMO, this is the best solution as it both simplifies interaction (reducing cognitive load by removing the "focus is in the places pane" hidden state) and optimizes it (reducing need to return to the file-browser pane).
2) Remove the Backspace keyboard shortcut for deleting entries in the Places panel and allow the rest of the window to handle it, similar to how the Tree and History panels handle backspace keystrokes. I can't see why this shortcut is even in the Places pane's code when it isn't used anywhere else in Nautilus.

Other information:
Steps to reproduce:
1) Open a Nautilus File Browser window from a standard install of Ubuntu 8.10 Desktop Edition. Ensure the Side Pane is showing(use F9 or View->Side Pane) and it is set to show Places in the Side Pane's drop-down. Also ensure that you have some bookmarks. These should show in the lower section of the Places panel.
2) Click on one of your bookmarks in the Places bar
3) Press backspace. At this point, the bookmark will be deleted, however the expected action would be that the main pane(file browser) would navigate up a directory.