Hi there.
I'm not sure I understand exactly what the issue is here.
You can disable the menu binds entirely by changing the plugin parameter in the plugin settings, 'Show in Menu' set it to false, and there will be no menu access to the plugin. The command that would show if this parameter is enabled is a catch all 'Crafting' command, which opens to a menu to select a category to craft in. It will only show categories that you have made recipes for already, and if there's only one category available, it skips past this window to go straight into whatever that was (cooking in your case).
If you only want to call a crafting scene from the map, set the 'Show in Menu' parameter to false, and ensure that you don't have any categories listed in the 'Category Menu Commands' parameter. There is no need to edit the plugin file itself for this.
If you want some categories to be accessible from the menu, and others to not, you can bind them individually using the 'Category Menu Commands' parameter, so you could bind cooking to the menu, and allow access to blacksmithing or alchemy only through an event on the map scene.
To call crafting from an event, use the plugin command, and set the category to the one you want to call. If you want it to call the category select menu instead, leave that parameter blank in the plugin command.
Let me know if you have any other issues.
~Ramza