Notwithstanding his belief in delayed animation and ensoulment, Aquinas still taught that abortion was wrong from the moment of conception. He believed it to be a mortal sin expressive of a homicidal will, even if in the early stages of pregnancy, as he thought, homicide isn’t actually committed.
Aquinas’s opposition, then, squares perfectly with the Church’s teaching, even if there’s a difference between why Aquinas thought abortion was wrong and why Catholic theologians and moralists today think it is.
Why did Aquinas believe ensoulment happened some time after conception? Because he accepted the science of his day, which taught the theory of the spontaneous generation of life (the idea that life spontaneously arises from non-living matter).
As applied to human reproduction, this theory suggested the (apparently) non-living elements contributed by each parent–“fetal matter” in the case of the mother and seminal fluid in the case of the father–were transformed from non-living matter successively into vegetative, animal, and finally human life.
Each of these stages was thought to come about by the infusion of a soul: vegetative life by the infusion of a vegetative soul, animal life by the infusion of an animal soul, and human life by the infusion of a human soul.
Since, according to Aquinas, the soul is the form of the body–that which gives life and makes an organism the kind of creature it is–if an organism possesses distinctively human qualities, we can concluded it possesses a human soul.
Because early scientists observed nothing distinctively human at primitive stages of human development (they knew nothing of genetics and possessed no microscopes), it was concluded no human soul was present.
Modern biology has shown the conceptus does have distinctively human traits. It is living and possesses a human genetic code to guide its growth and development. If Aquinas had had the benefits of this knowledge, his principles would have led him to conclude ensoulment occurs at conception.