So shalt thou put away the guilt of innocent blood from among you,.... Which otherwise, the person not being found out, and brought to just punishment for it, would devolve upon the whole. Aben Ezra interprets it the punishment of innocent blood, which, by the above method being taken, would not be inflicted on them:
when thou shalt do that which is right in the sight of the Lord; as it was to observe this law concerning the beheading of the heifer, with all the rites and ceremonies belonging to it here enjoined; as well as every other command, statute, and ordinance of the Lord, which are all right to be done, Psalm 19:8.

In this way Israel was to wipe away the innocent blood (the bloodshed) from its midst (cf. Numbers 35:33). If the murderer were discovered afterwards, of course the punishment of death which had been inflicted vicariously upon the animal, simply because the criminal himself could not be found, would still fall upon him.