Are base runners always protected on a illegal pitch?

[roadking]

Originally Posted by marvin

NFHS - The coach does not have a choice of the penalty or the play unless the batter does not hit the ball (fair or foul) or otherwise become a base runner.

Ok,
Then on a hit and run (swing and miss), baserunner takes off for second and draws a bad throw form catcher, baserunner advances to third.

Options for the offence:
*Take the results and keep runner on third.
*Take the ball on batter and put runner back on second.