Do You stop it?

[The Roamin' Umpire]

Clearly, once you have a dead ball, you should kill it no matter what happens between your decision and the whistle. Whether or not I personally succeed in doing this is tough to say - I haven't been specifically watching for it.

Here's a dramatic example: One game I did at HL, the QB was wrapped up in the end zone, but still struggling. He got a forward pass off, and then about two seconds later I hear a whistle from the R. He ruled that progress was stopped in the end zone and awarded a safety.