I am not sure exactly how you would do this but you seem to know about ASM or reverse engineering (reflection?) so you could probably do this with a bit of effort.

I am proposing that this mod stays the same by itself but if CraftTweaker/MineTweaker is present then it would also add the ability to add or remove recipes from certain Witchery devices.

On the most basic level Cauldron crafting, Kettle crafting and Oven sapling support. Providing hooks to recipes for these devices along with custom commands to be used in .zs scripts could allow to add, remove or change Witchery recipes for these devices (by removing and adding them back as a custom recipe) .

More advanced would be Circle Magic rituals and Distillery to add or remove recipes.

Other devices would be Brazier and Spinning Wheel to add or remove recipes.

Also consider my other proposal:
#4