Can't you just choose not to craft the seeds?
That I can do, but I'd rather just disable the generation if at all possible. Would just be useless clutter if I didn't. Just trying to figure out this config file. As it looks different from what John E. posted above.
general {
I:"Change crafting modes, 0 = Normal(Default), 1 = Hard & 2 = Hardcore"=0
I:"Change number between 1-100 for chance of getting second seed drop, 10 = 10%, 20 = 20%(default) and so on."=20
I:"Change to disable or enabled second seed drop, 1 = Enabled (Default), 0 = Disabled"=1
I:"Disable Crafting for Magic Fertiliser, 0 = Enabled(Default), 1 = disabled"=0
I:"Disable Crafting for Magical Books (Magical Books, Infused Pages, Infused Leather), 0 = Enabled(Default), 1 = disabled"=0
I:"Disable Crafting for Magical Items (Natures Gift, Dark Star & Obsidian Skull), 0 = Enabled(Default), 1 = disabled"=0
I:"Enable or disable chance of getting Magic Essence from Magical Crops, 1 = Enabled (Default), 0 = Disabled"=1
I:"Enable or disable particle effects on crops, 1 = Enabled (Default), 0 = Disabled"=1
I:"Use old 16 x 16 textures for Magical Crops, Disable(Default) = 0, Enable = 1"=0