I'd go buy some inexpensive gold fish and put them in, sometimes you can find people selling/giving away goldfish like on craigs list. If you buy feeder ones Mr Turtle may eat them
You can also put minnows in there as a test or to just keep skeeters out, the turtle may eat those too but if you provide places for them to hide and buy a dozen or so to begin w they breed quickly. It is very unlikely your turtle caused this. Goldfish get tumors sometimes, I've had them do that too. I would not break down the pond and scrub it all out, you will lose all the bacteria and so forth, will turn into a mess. There is no need to kill your turtle, he did not cause this. When you buy new fish, put them in a tank for 2 weeks and watch to make sure they don't have anything wrong with them that needs treated (ich ect) then add them to the pond. If you are getting goldfish from an already established pond-all the same place, you won't need to do this. Be careful treating fish IN the pond as the meds may harm your turtle.