So if you don't absolutely need to over-ride their navigation, don't do it. Instead, call manilaSuite.plugins.getStorageAddress. Pass your pluginName as the parameter. Your plugin shouldn't assume any specific location for site-specific storage. Your plug-in gets the address of a table and can do whatever it wants inside that table.
Manila handles making sure that the table is stored within the site.
Within that table are two sub-tables, data and enabled. But you should write your code as if that may change at any time. Always call manilaSuite.plugins.getStorageAddress. Your config table should contain an item named disableScript. Again, it uses manilaSuite.plugins.getSiteFragmentAddress to get the address of the website fragment, then deletes it.