Here is how you can remove the recipe from the game.
ForgeRegistry<IRecipe> recipes = (ForgeRegistry<IRecipe>) ForgeRegistries.RECIPES;
recipes.remove(new ResourceLocation("minecraft", "furnace"));
Though you will need to re-add the recipes after a disconnect. Though if you send the packet in the correct event it will sync your recipes correctly.
On the other hand you could create your own IRecipe implementation that references your config variables and return accordingly in matches and getCraftingResult.