A question came up in discussions about the PK whereby the signal was given and the ball actually kicked when a teammate of the kicker punched an opponent while the ball was in flight. The discussion was mostly to immediately blow the whistle, stopping the kick, deal with the violent conduct and retake the kick. Since the incident was serious and could have led to other issues, the feeling was stop play immediately rather than let the kick conclude. Then since the kick was stopped, to come back and retake the kick with the thought that the initial incident leading to the PK still needed to be addressed.
USSF answer (September 28, 2011):
The ball is in play. The referee would deal with the serious foul play and, after sending off the kicker’s teammate, restart with a direct free kick for the defending team.