I explained this in a previous post called Shortstop Mistakes as it related to a normal double play. It applies to throws by the pitcher on the 1-6-3 double-play as well. First, the shortstop must begin at double-play depth (double-play depth is explained in this post) in order to get to the bag in time to turn a double-play. When the ball is hit back to the pitcher, the shortstop should take a couple big, quick steps towards the bag to quickly cut the distance between him and the bag. Next is the tricky part. When the shortstop gets to within 5-6 feet of the bag, he has to slow down using smaller steps in order to read the throw from the pitcher. I refer to this as "sneaking up on the bag." If the throw is on target and over the bag, the shortstop continues moving quickly again, catches the ball over the bag, and makes the throw to first base to complete the double-play. If it's a poorly thrown ball on the third base side, the shortstop can stop, catch the ball, and then go to the bag.
The point is that the shortstop has to try and stay behind the ball so that he is always moving towards second base when he catches the throw. This allows the shortstop's momentum to continue through the bag even though the pitcher's throw may not be a great one.
If the footwork and timing is correct, a shortstop - unless the throw is just horribly off target - should never have to reach back to catch a throw from the pitcher.