Players may want to disable certain harvestcraft blocks to add additional challenge or maintain balance in a modpack. For example, water in my pack is usually a finite resource that must be managed, so being able to disable the well would be helpful.

mods.jei.JEI.removeAndHide();

That is the template for effectively removing an item from survival using crafttweaker. Of course it doesn't actually remove it from the game because you can still access it in creative, but balance doesn't exist in creative anyway.