Im not sure how to remove a recipe but you can overwrite the with something else e.g.
CraftingManager.getInstance().addRecipe(new ItemStack(Blocks.cobblestone),
"CCC",
" S ",
" S ",
'C', Blocks.cobblestone, 'S', Items.stick);
This will give you a block of cobble when you try to craft a cobble pick.
This may not be the best way to do this.