Coach's Options on Balk

 
With one out and runners on first base (R1) and second base (R2), the pitcher balks (fails to come set), but still throws the pitch. The batter (B1) hits a double to centerfield. R2 scores easily. R1 is thrown out on a close play at home. B1 is safe at second base.
 
The defensive coach wants the balk enforced (R1 and R2 advance one base, B1 remains at bat).
 
The offensive coach would like the option to take the results of the play (one run scores, R2 is the second out of the inning, and the batter ends up at 2nd base).
 
If playing under NF rules, is there an option? What does the umpire do?
 
Bonus Question: If playing under NCAA or MLB rules, is this handled differently?
 
Call
In NF, when the pitcher balks, the ball becomes immediately dead. All runners are advanced one base and the batter remains at bat (NF 5-1-1K and 8-3-1a).
 
If the game is played under the NCAA or MLB rule set, the ball remains live on a balk. If all the runners and the batter advance one base on the pitch, then the balk is ignored. If they do not, then the balk is penalized in the same manner as the NF rule set.
 
The coaches do not get the option of taking the play or penalty in any of the rule sets.
 
In the play below, in NF, the ball is immediately dead, R1 and R2 are awarded their next base, and B1 remains at bat. In NCAA and MLB, since all the runners and the batter advanced at least one base on the pitch, the balk is ignored.