An umpire's perspective: if the pitcher throws to an unoccupied base from the set position, it needs to be a bona fide attempt to get a runner out.
Think about the timing of this play.
If the runner starts as soon as the pitcher picks up his non-pivot foot and the pitcher throws to second as described in the OP, how far will the runner have advanced? If the runner sees the throw go into second before he has taken more than a few steps and safely retreats to first base, many umpires will be disinclined to call the throw to second an attempt to get the runner out.
If there's not a play at second, it's going to look more like an attempt to force the runner to retreat than to get him out, and there's a good chance it will be ruled a balk.