Yes, it would be a good idea to exclude it.
Internally, the teleportation cycle is just a crafting machine running a recipe with one input and no outputs. The s6x-teleporrter-input item is designed to rapidly spoil so that if you activate a teleporter that isn't going to work, due to lack of power or whatever, the item just disappears, rather than sitting there in the input slot. If it doesn't spoil, the useless items will start to pile up.