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.

So shalt thou put away the guilt of innocent blood from among you, when thou shalt do that which is right in the sight of the LORD.

21:1-9 If a murderer could not be found out, great solemnity is provided for putting away the guilt from the land, as an expression of dread and detesting of that sin. The providence of God has often wonderfully brought to light these hidden works of darkness, and the sin of the guilty has often strangely found them out. The dread of murder should be deeply impressed upon every heart, and all should join in detecting and punishing those who are guilty. The elders were to profess that they had not been any way aiding or abetting the sin. The priests were to pray to God for the country and nation, that God would be merciful. We must empty that measure by our prayers, which others are filling by their sins. All would be taught by this solemnity, to use the utmost care and diligence to prevent, discover, and punish murder. We may all learn from hence to take heed of partaking in other men's sins. And we have fellowship with the unfruitful works of darkness, if we do not reprove them.