[BoomerSooner]

As a BU, how would you have handled the same situation with the exception that the ball went into fair territory after contacting the bat? Having "clearly" seen the ball contact the batter would you allow the play to continue even if the plate umpire is pointing toward fair territory? Regardless of whether the ball hit the player then bat or bat then player, the ball contacting the batter creates a dead ball. If there is any debate beyond that, you can have that discussion after calling a dead ball because nothing will change the fact that the ball was dead when it hit the player.

Bringing this back to the OP, I think you can probably answer the question based on how you would handle my example. I say that because this is a situation I bring up with my partner in pregame (albeit we usually discuss it with regard to a normal swing that hits the batter). My preference and what I request of my partner is that he/she kill it if they are sure the ball has hit the player. After that give me a sign if it is complicated enough to need discussion. Conversely, I've had some partners tell me to leave it alone when I'm on the bases and that is what I do. To me realizing you can't see everything from behind the plate and having a plan on how to deal with it is the key.