Not only can intelligent design and birth defects be reconciled, they have been.
The Intelligent Designer did not take upon Himself human flesh for any reason but to reconcile the world to Himself.
The root of all birth defects is sin. The Intelligent Designer became sin on behalf of His creation, thereby reconciling the world to Himself.
So it happens that the Intelligent Designer's desire, above all things, is to show Himself as merciful, slow to anger, and abounding in grace and mercy. That's just one reason He does not intrude upon His creation in ways we might expect.
His is an everlasting mercy that applies to the best and worst of all creation from generation to generation.
BTW, that's what Christmas is all about, Charlie Brown.
Is ID a religious doctrine or a scientific theory? This is the heart of what is being argued in courts, election campaigns, etc. I'm interested in the scientific point of view.