To stop the synchronization of your top and quick launch navigation and of the default homepage the Collaboration Manager contains a simple solution. With this settings only the new added menu items will be added to your menu.
The existing menu items and the existing homepage wouldn't be overwritten.
Choose the workspace whose naviagtion synchronization should be stopped and select the "Site Settings".
Now select the "Synchronization settings" in the "Collaboration Manager" tab.
Now you can set the hooks and the synchronization will be disabled.