Did God commanded genocide?

A common method to cast doubt on Christianity is to proof text (in a fundamentalist type of way) passages that show that God commanded genocide or some other atrocity. I have never met a Christian who has interpreted these passages as such. Viewed within the context of the Bible, God is ruthlessly just but this must be learned first before his mercy can be fully known. Taken in isolation these passages do become problematic. I think that William Cowper’s poem "God moves in mysterious ways" speaks to this difficulty.

Judge not the Lord by feeble sense,
But trust him for his grace;
Behind a frowning providence,
He hides a smiling face.

His purposes will ripen fast,
Unfolding every hour;
The bud may have a better taste,
But sweet will be the flower.

Blind unbelief is sure to err,
And scan his work in vain;
God is his own interpreter,
And he will make it plain.