Good point, good idea. Added in new version 1.1.0
It has to be a startup mod setting and not a runtime change, as the recipes are being hidden at creation with the "hidden" flag and the game must be re-started to access this.
Even if I find a way to do it at runtime, recipes are stored across the force, so in MP it'd be hidden for everyone or noone and changing it would reload all recipes across everyone - it sounds like a bad idea, but I might keep looking into it xD.
IMO best method to avoid havoc in the pipes would be to remove the pipes before changing the recipe ;D