The issue of this article was never whether waterboarding or other measures are a useful national security tool. The question was whether it is a Christian choice, one Jesus would approve.
Neither the article nor the comments has been persuasive on this point.
As to what Jesus would do in a specific situation, we can only guess, based on our understanding of Him.
Jesus said love your enemies, not let them kill you. Jesus said to forgive those that wrong you, but this is an individual command, not one for governments charged with protecting their people.
Besides, forgiveness requires repentance, which seems to be lacking among Islamists.
Anyway, one day He will explain it to us Himself. Go with His Peace.