IMHO - If the shooter was fouled in the act of shooting and the horn sounds before the release of the shot you have no basket and the shooter gets two free throws.
If the shooter was fouled in the act of shooting and the clock stops on the foul - which, by the way, probably means the whistle and the clock operator both anticipated the foul - I think you allow the basket and award one free throw. Trying to convince the participants that your definite knowledge indicates a timing error (the horn should have sounded before the release) would be a real stretch of your credibility.
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