This writer, Katherine Steward, seems to display extreme bias and slanted stories against Christians. No true follower of Jesus Christ would be teaching or promoting any kind of genocide as the president of CEF has stated. The gospel, which is the focus of the CEF organization, is the message of God's love through Christ for all people.
So, your operating premise is that
everyone who promotes and teaches Christianity is, by default, incapable of promoting any kind of genocide,
and that anyone who accuses such people of doing so is automatically suspect.       Not that you're biased or anything.
If you note, Ms Stewart pretty much explains herself in her reply to Reese Kauffman, President of CEF, when he tried to clarify the lesson.
"
Katherine Stewart replies:
Though I welcome Mr Kauffman's comments, I regret to note that he seems to be unfamiliar with his group's teaching materials. Nowhere in the lesson plan on the Amalekites does the CEF mention the "New Covenant" and its prohibition on genocide. Mr Kauffman claims the CEF "would never teach children that God would instruct them, or anyone today, to commit genocide". And yet the CEF's lesson plan on the Amalekites tells children that God wanted Saul "to go and completely destroy the Amalekites people, animals, every living thing". It also repeatedly tells children that the Amalekites deserved punishment for their "sinful unbelief".
To be precise, the thrust of the CEF's lesson is to teach obedience that if God tells you to kill unbelievers, or do anything else for that matter, you must do exactly as he says. "King Saul should have been willing to seek God for strength to obey completely," the lesson plan on the Amalekites reads, and in three separate places it instructs teachers, "Have children shout 'God will help you obey!'"
There are many ways to teach the Christian faith to young children, many of which do not involve teaching obedience through the tale of the genocide of the Amalekites. Readers of the Guardian and parents of American school children are entitled to know which variety of the Christian religion the CEF is promoting in its public school clubs."
source
So I believe Stewart hit the nail on the head. In essence, one of the the CEF messages comes down to:
God always does good
God visited genocide upon the Amalekites
_____________________________________
Visiting genocide is a good thing
What is particularly galling about this is that preachers often have no trouble interpreting scripture as they choose and telling their parishioners what god wants and expects. So all we need are children growing up with "obey god" tucked back in the recesses of their mind and some knuckle-headed preacher coming along and telling people about the marching orders he's just received from god. The brain-addled follower may well start thinking
"Hey, if something like genocide was okey-dokey with god back in who-knows-when, and he now wants us to get rid of all the X people, Why not?"
And all that's left to do now is
"Have children shout 'God will help you obey!'" 
On the other hand.
The Amalekite genocide story does point up god's lack of morals.
Of course, if anyone wants to defend genocide or just "put[ting] to death men and women, children and infants, cattle and sheep, camels and donkeys,'"
* be my guest. I'm listening.
* NIV.
