Pythagoras needs the units to be the same to calculate the actual length of the pipe, so since you probably want to have the result in kilometres let's convert those elevation metres to elevation kilometres.
Change:
PipeActualSpillLength = ((D1 - D2) ^ 2 + (E1 - E2) ^ 2) ^ 0.5
to:
PipeActualSpillLength = ((D1 - D2) ^ 2 + (E1 / 1000 - E2 / 1000) ^ 2) ^ 0.5
(and don't forget to recalculate column D afterwards).