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The Incinerator destroys any items that are pumped into it, whether with BuildCraft Pipes or RedPower Pneumatic Tubes.
However, there are more useful ways to utilize extra materials. They can be Transmuted or Condensed for items of higher value, or used to create Scrap with a Recycler for use in a Mass Fabricator or be used to make Fertilizer in the IC2 Farming Section. Although it is true that you can Condense and Recycle items, if an item has no EMC value and you don't have a sufficent source of EU, this can be useful to get rid of excess. Its main use is preventing overflow (in combination with an advanced insertion pipe) when using BuildCraft pipes without creating extra network lag. However, if you are using Redpower pipes, this is not really a necessary item and using one is not a recommended way getting rid of waste. It can be used to keep Quarry-connected chests from overflowing if too many items pile up, such as Dirt or Cobblestone, which appear in abundance.