I'm convinced that the decisions they made were made with the knowledge they had at the time, and to protect the women who miscarried or had a late period.
All too often, these arguments are made by the same people who ridicule religion for insisting that the sun revolved around the earth. As though none of the geocentrists were the equivalent of scientists. And, they're hoping we don't remember the way Medicine resisted the germ theory and the way that Semelweis was treated by the hierarchy at that time. Or, more recently, the difficulty in convincing Medicine that folic acid was vital to neural tube development, that breast feeding really is best, that heart disease is really due to a bacterial infection and that cervical cancer is an STD.
We should all remember that science develops better tools, with finer measurements all the time. Knowledge simply increases, often before we know what we're doing. It's hard to let go of the old pardigms -- especially if someone's reputation (or Lord forbid!) research grant is at risk.
We now know what happens when a sperm and an oocyte fuse. We especially know which embryos in the Petri dish are alive and which are not embryos or which are not dividing.
Extrapolating from "water" in the womb that can't be measured or verified to "water" in the lab - petri dish or, soon, the artificial uterus - after a deliberate act of creation is simply wishful thinking. And it goes against scientific knowledge.
Why? Do you think they did not understand the basic concept of "conception"? The issue was not the scientific knowledge today that did not exist then. Their rationale was not based on any lack of knowledge since the reasons given by them (unformed body and lack of animation)were in fact actually how the fetus is formed. Nor am I aware that Pope Pius IX was aware of any new scientific knowledge. Since the very existence of the soul itself is based on theological or philosophical conclusions, no amount of scientific knowledge can support its existence at any stage of development. Faith must substitute for proof.
For those who do not have such faith, abortion can still be opposed on constitutional grounds.