I agree with the input that Schmidt enlightened us with. I have been involved with several leagues that handle the free throw situation the same and there has never been any issues. It allows players to still shoot free throws (which is a part of the game), but also it doesn't waste that much time especially if it is running clock. Lastly it avoids any issues that might happen towards the end of the game if the game is close. Free throws are important to have down the stretch and it allows the team that is behind to still have a change rather than just giving the other team points without earning them.
One free throw for 2 or 3 points and if they make the bucket while getting fouled just add a point automatically as it is an and one. As long as you explain the rule at the beginning there shouldn't be any issues.