Easy to fix the problem of ppl dropping the wrong siege on top of the right one. Allow the player to select the type of siege they will build. in a ui pulldown or even add that function to the commander tag. Only this siege can be built in a radius of x around the commander tag.
That way a balista dropped onto a ram in front of a door would not get built.
Next, allow siege to be salvaged. make it a wvw skill with more salvage per point. To control supplies attach a hidden counter to any siege that diminishes the supplies that can be salvaged based on the amount of damage it does. That way genuinely used siege return a little, unused siege returns a lot.