They did that to isolate grounding for key in ignition buzzers, time delay lights and other fancy stuff. You can isolate the grounds using diodes and sharing a lug on a two lug switch. It was cheaper for the factory to make a three lug switch than add a couple of diodes to keep the circuits from talking to each other. Also lowered the parts count and increased the time before failure.
To hook them up, get a female lug of the same size as the switch. Hook the two cathode ends of 1N4001 diodes to the lug and hook each anode end (the one with the white stripe next to it) to each of the two wires from the harness. You can get the diodes or a substitute from Radio Shack. Total cost of all the lugs, spades and diodes will be less than ten bucks.
Craig