John Gill Commentary Deuteronomy 21:9

"So shalt thou put away the innocent blood from the midst of thee, when thou shalt do that which is right in the eyes of Jehovah." — Deuteronomy 21:9 (ASV)

So you shall 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 you shall 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, (Psalms 19:8) .