In the case of using Minetweaker, its not a recipe that you have to find and remove in that sense, rather, you add a command in a minetweaker script, an example is given below:
Code:
recipes.remove(<minecraft:stick>);
Except in this case, instead of minecraft:stick, you need to find the correct item ID for the Rod of the Skies. You can do this (at least in the versions I've used) by going into creative and holding the item in your hand, then typing "/mt hand" in the command line - that should give you the correct ID.
Needless to say, you need to have the Minetweaker mod installed for this - I would also recommend familiarising yourself with using the mod, looking at some basic tutorials.
As an alternative, certain mods have within their config file the option to disable items individually - Actually Additions is one such example - in the case of AA, you change the value after the = sign from true to false. It might be worth looking in the configs folder for Botania.cfg, and looking in there to see if there is an option. Someone more familiar with Botania's config file might be able to correct me on this!