A pitcher may throw to an unoccupied base only if it is an attempt to retire a runner. In your scenario, assuming F1 makes a legal move to 2nd and the runner continues to 2nd, it's a legal move.
If the runner sees F1 throwing to 2nd and returns to 1st, it's a balk.
If F1 steps toward 1st, he must throw there.
If you see a runner breaking, step off. If there are no other runners, you should get him 100% of the time.