What is the ruling on killing an infant born with a congenital malformation (incomplete skull bones and protrusion of the brain), and what are the consequences for the perpetrator who has repented and regretted his action?

What your sister's husband has done is a grave sin. Intentionally killing a believer is punishable by Hellfire, God's wrath, His curse, and a tremendous torment. It is the first matter to be judged on the Day of Resurrection. A believer remains righteous as long as he does not shed unlawful blood, and the perishing of the world is less significant to God than the unlawful killing of a believer. If the killer repents sincerely, his repentance will be accepted. The father is not killed for his son according to the majority of scholars, but he is obliged to pay blood money to the son's heirs, from which he inherits nothing.