[BoomerSooner]

It was changed prior to the 2013 season and was largely pegged as an attempted to reduce the length of games/increase the pace of play.

Regarding the OP, the pitcher could have completed his throw to 3rd (instead of faking), and as you stated there wouldn't have been a penalty for throwing to an unoccupied base because he was attempting to make a play (the exception to the unoccupied base rule). The other way to defend this is to have the pitcher disengage the pitcher's plate prior to making a play on the runner.

I felt like the worst dad in the world when my 13 year old got called for a balk this spring because I hadn't coached him on how to handle a very similar situation (neither had his coach, but that's a different story). With runners on the corners, my son came set and the runner from 1st took off toward 2nd at a fast jog. My son being left-handed saw this unfolding and lifted his stride foot and turned his shoulders toward the runner. I could tell he knew he had messed up from the look on his face, but he tried to cover it by making it look like he was coming set (which he couldn't really do because he was already set, although sadly, the umpires let him throw a pitch in spite of the delay between the actual balk and when he threw the pitch). I'm betting the play was designed to draw a balk, and if not draw a throw to allow the runner from 3rd to score. Had my son properly disengaged the pitcher's plate and ran toward the runner, the offense would have had a more difficult time scoring that runner from 3rd. I'm even willing to bet the runner from 3rd would have taken off for home on a good solid fake from my son.

The point of this whole story is that a pitcher in the set position prior to starting the throwing motion almost always benefits from disengaging prior to making a play on a runner that has left before said motion starts because there are no restrictions on him at that point. He can run at the runner, fake a throw or throw to any fielder anywhere on the field.