While the answers given here are right for the HS game, this is where (once again), I think the NBA rule is better. In the NBA, anytime the ball is legally touched inbounds, a minimum of 0.2 seconds must come off the clock. The reasoning (which is correct, IMO) is that if the ball is touched, then the clock must start and stop.
In the original case of this thread, it's simply not fair to allow the throw-in team to advance the ball the entire length of the court with no time off the clock. But since in HS and NCAA, we don't have definite knowledge of how much should've come off, we can't do anyting about it.