Make the fouls hurt more, you broke the rules, the penalty should hurt. How about when you are in the bonus you get a free throw and the ball, in the doulbe bonus you get two FT and the ball.
For shooting fouls before the bonus you could give the coach the choice of freethrows or the ball. That way you can't force a 17% free throw shooter to the line with hack a Shaq. It also avoids the need to put good free throw shooters in at the end of the game, often creating a size disadvantage, let the best players play and win the game on their merits.