This probably isn't written in any rule book, but the referee (the one in the white hat that is positioned behind the offense) is the one to make that call. If the kick is away and the punter has ended the punting motion, has both feet on the ground, has his balance, is attempting to pursue the ballcarrier, and isn't vulnerable to injury (as he would be with his kicking leg way up in the air and the other leg planted) then the referee is going to know that its a block. I'm pretty sure that the running into / roughing the kicker is meant to avoid injury when the kicker is vulnerable. The kicker should know that it's a contact sport and when the kick is gone, he's gonna get nailed. The officials should realize the difference and let them play.
There is also the case when a player is blocked into the punter by the punting team. If a defensive player is blocked, pushed, or thrown into the kicker by the punting team, there is no penalty.