Obstruction followed by Deliberate Crash

"I had a call where I called obstruction on the catcher on a play at home as he did not have the ball, and R3 who was coming home at the time, took the catcher out with his arms up and scored. I called dead ball, ejected R3, put the other runners back etc., but scored the run."

In Canada  we have allowed the run to score because it does not fit the requirement of the crash rule in that the catcher does not have the ball. ASA and ISC (they use ASA rules) they do not count the run. They call the player crashing out.  In this Case play it is important to remember the catcher does not have the ball. The crash rule 8-9 s (old rule book)  says the defensive player has the ball and is waiting for runner and the runner remains on his feet and delibertly crashes into the fielder, then the ball is dead and the runner is out.
 
The key to our interpretation is the catcher does not have the ball. He is not allowed to block the base and is charged with obstruction. We say call the obstruction. If the crash is flagrant call: Time-award the run and eject the player. All other runners return to the last base touched at the time of the stoppage of play. As far as I know that is how the ISF rules also.