To stop the synchronization of your top and quick launch navigation 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 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.
Set both of the hooks and save it with the button "Ok".