http://iscoresports.com/

runner on 2nd, batter grounds to SS. SS checks runner at 2nd, then throws to 1st for a 6-3 out. As SS commits to throw to 1st, runner on 2nd heads to third and is safe- no throw.
How is this scored? Advanced by batter, stolen base or fielders choice?

There is an option for "On the Throw" as a way for a runner to advance bases. This sounds like it would fit for what you are describing.