Unless I somehow missed it, there isn't a way to get rid of crafted waterway item. In Krastorio2, there's the Crusher building, which allows you to void a lot of items to get rid of them. It does that by auto-generating a voiding recipe for every item in the list:

-- For each item load that can't be produced by crushers
-- will create a recipe that give 0 void item consuming the input

-- creating void crushing recipes
for _, type_name in pairs(krastorio.items.item_types) do
  if type_name ~= "fluid" and type_name ~= "module" then
    for item_name, _ in pairs(data.raw[type_name]) do
      if not crushing_ingredients[item_name] then
        data:extend({
          {
            type = "recipe",
            name = void_crushing_recipes_prefix .. item_name,
            icon = kr_recipes_icons_path .. "trash.png",
            icon_size = 64,
            category = "void-crushing",
            hidden = true,
            hide_from_stats = true,
            energy_required = 2,
            ingredients = { { item_name, 1 } },
            results = { { "kr-void", 0 } },
          },
        })
      end
    end
  end
end

(where item_types is this list:)

krastorio.items.item_types = {
  "ammo",
  "armor",
  "capsule",
  "fluid", -- But why
  "gun",
  "item",
  "mining-tool",
  "module",
  "tool",
  "item-with-entity-data",
  "repair-tool",
}

Since the waterway is of rail_planner type, it can't be voided in the crusher (putting it in the crusher gives you the message "Straight water way cannot be smelted"). I don't know if this would be the best way of solving this, but I think adding a specific recipe for voiding water ways (as a K2-compatibility thing) would be great.