This is a most ambitious topic, but your look at Benedict is too cursory and your skim of Judges deploys way too attenuated logic and no heart-felt clarity.  I think the most important beginning point is Jesus of Nazareth, who, unlike us, had no new testament to fall back on.  He knew all too well the hard-hearted portions of scripture and knew how the pharisees of his day who, if allowed, would attempt to write their own additions to scripture under dualistic, punitive, vengeful and triumphant themes.  Time and time again, Jesus repeats a phrase found frequently in Hebrew scripture when someone encounters the Father: "Be not afraid."  Jesus is the one who refuses to condemn the woman caught in adultery, he offers the father of the prodigal son as a likeness for his Father, and he, in the middle of torture and death, pleads for persecutors to be forgiven.    Let us anchor ourselves there before venturing into the seemingly petty and punitive creator described in the Great Flood, or in 1 Samuel, Chapter 15, or in Exodus 32:25-29 (none of which can be explained away by the principle of voice).  Since Jesus is so thoroughly devoted to the Father, we must summon the grace to suspend our human logic and endure the apparent incongruity of these "dark" passages.