Changing Call Outcomes

[commcoach]

Hi everyone. I was recently just turned onto this forum from another site. I should maybe provide a little background; I've played various forms of organized basketball for over 15 years. By various forms I mean jr high and high school teams as well now in a competitive men's league team. On top of that I have been coaching a community basketball team (register and play, no tryouts) ranging in age from 12 to 19 years for the last 8 years.

I posted this scenario in the previous forum I mentioned, and thought it would be beneficial for me as both a player and a coach.

We all know that once a ref makes a call, it sticks. But what if the call resulted in a misapplication to the consequences?

Player on my team gets the ball at about mid-post where he is then double teamed. The ref watching the backcourt blows the whistle as the offensive player shoots the ball as the ball goes in the hoop.
The call: Foul on #XX. Basket's no good. 2 shots.
This was the defensive team's first team foul of the quarter, so there could not have been a bonus. I approach the ref asking for an explanation of the call, but he immediately shut the door on me.

It didn't occur to me until after the game, but I'm thinking I maybe should have called a timeout in order to buy some time to get this sorted out by the refs. We are a poor free throw shooting team, so I would've much preferred the basket+1 rather than just the 2 foul shots. If I called the timeout, what could the change have been?
A) Foul counts. Basket counts + 1 free throw?
B) Foul counts. Basket doesn't count. Offensive team's ball on the baseline?

Is there anything I could be missing? At this point, it's still a correctable error and I'm asking for is an explanation as to how we can be rewarded 2 free-throws for getting fouled in the act of shooting AND not have that basket count? As an official, how would you prefer this situation be handled? I know there are varying rules for different regions, so let's just say we're following FIBA rules.