Horn sounds during free throw

[Burtis449]

National Federation Rules.
Visiting player B1 is on the free throw line with less than a minute to play down four (4) points with two (2) shots due to personal foul by A1.
With the ball clearly still in the hand of the shooter (B1) who is in his shooting motion, the horn is sounded by the table! B1 continues with his shooting motion and the ball goes in the basket.
[The table informs us that the foul on A1 was his fifth foul]
Now what is the proper procedure. I need a rule or case book referance for this instance.
FYI, we allowed the free throw to count, got the sub in for the disqualified A1 and then went on to shoot the second foul shot and then went on with the game. This seemed logical to us but we are pretty sure that there is a specific way to handle this unusual situation.