Killing the turtle is not going to do a bit of good. Your pond is good habitat for a snapping turtle, so when that big one leaves, it will just make it easier for a new one to move in. Besides the fact that just is senseless and unfair.
Our neighbor has a little pond, about half an acre, with all different kinds of fish in it. He has tried twice to have ducks, but there is a MASSIVE snapping turtle in it. Ate all of the Rouens, then all six Pekins when he tried to have ducks again. They were full grown ducks, too. And it was...