Then said he to Zebah and Zalmunna, What manner of men were they whom you killed at Tabor? They answered, As you are, so were they; each one resembled the children of a king.
In Gideon's case, God's Word specifically commanded him to execute vengeance upon the murderers of his brothers.  The institution of the "cities of refuge" was not for the purpose of protecting willful murderers from their just punishment, but in order to protect the unintentional manslayer from the avenger of blood.  "It was the duty of the nearest relative to execute vengeance upon the murderer of his kin; he became the [~go'el]."[20]  In this light, Gideon's execution of his brothers' murderer is exactly what God had commanded him to do.