It seems the GMarkerManager Class in the current version of the Google Maps API doesn't do useful things like allow you to remove markers from a manager instance or clear them all. Luckily, it looks like such functionality is being incorporated into a future version, as described here
At date of writing, the extra functions described in the link above are not available through the main GMap2 class, but instead must come from an instance of MarkerManager as shown in the example's source code. Include this javascript in your code and create an instance of MarkerManager: