Here's my issue with that logic for continuing the routine:
If you carry that logic to a larger competition that carries more weight in the year than a first competition like this one, you're scoring a team missing 2 athletes. If this exact incident occurred at Worlds and those involved used the logic "the injuries are off the floor," this team has to then compete their pyramid, baskets, stunts, etc., without 2 members, which I'm assuming would effect their score.
Secondly, when did this whole "the injuries are off the floor" logic begin? Seems like a way to cover your behinds, because I have seen routines stopped at almost every major competition whether the athlete has left the floor or not, and there were plenty of instances where the athlete had left the floor before the music was stopped.