Here's the rule:
(6) a fielder unsuccessfully attempts to put out a preceding runner and, in the official scorer's judgment, the batter-runner would not have been put out at first base by ordinary effort.
Rule 10.05(a) Comment: In applying Rule 10.05(a), the official scorer shall always give the batter the benefit of the doubt. A safe course for the official scorer to follow is to score a hit when exceptionally good fielding of a ball fails to result in a putout.
(b) The official scorer shall not credit a base hit when a:
(1) runner is forced out by a batted ball, or would have been forced out except for a fielding error;
(2) batter apparently hits safely and a runner who is forced to advance by reason of the batter becoming a runner fails to touch the first base to which such runner is advancing and is called out on appeal. The official scorer shall charge the batter with a time at bat but no hit;
(3) pitcher, the catcher or any infielder handles a batted ball and puts out a preceding runner who is attempting to advance one base or to return to his original base, or would have put out such runner with ordinary effort except for a fielding error. The official scorer shall charge the batter with a time at bat but no hit;
(4) fielder fails in an attempt to put out a preceding runner and, in the scorer's judgment, the batter-runner could have been put out at first base; or
Rule 10.05(b) Comment: Rule 10.05(b) shall not apply if the fielder merely looks toward or feints toward another base before attempting to make the putout at first base.
(5) runner is called out for interference with a fielder attempting to field a batted ball, unless in the scorer's judgment the batter-runner would have been safe had the interference not occurred.
So, if the scorer judges that, when the attempt to put out the preceding runner is unsuccessful (ie, the runner is safe), the batter would have been safe if the play was made to first, then it can be scored a hit. If, in the scorers judgement, the batter would have been out if the play had been made there, it would be scored a fielders choice.
It's a judgement call. You really had to be there, but it's not automatically a FC when the runner is safe just because the play was made at 2nd rather than 1st.
Hope this helps some.