: How can you humanize infanticide of the evil-tainted? The world is surrounded by an alternate realm called the spirit world. Humans existed as separate physical entities, but maintain an attachment

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I think, to humanise infanticide, you can present the whole thing as the terrible tragedy it is: the parents would have done anything to prevent this situation, they would accept any sacrifices to avoid this now, but there's simply no choice. They are shattered by what they must do. They are deeply traumatised by this afterwards (something which may take many different forms). But there is no alternative open to them.

Why there's no alternative? That's up to you. But the thing is, do not ignore the implications, the tragedy. Don't make it easy - that would be inhuman. Instead, accept and explore how terrible of a reality it is.

Since that's the way any reader would see such a reality - terrible and painful, it would be easier for the readers to sympathise.

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Be aware of snuffing disabled children

The "deformed" babies excuse is not going to win you any friends who are disabled (estimated 15% of the world's population, as high as 1-in-5 in 1st-world countries with aging populations). I never realized how pervasive this trope is until I heard this talk about zombies from a disabled person.

Consider how you describe the "visible signs" with some consideration for all the "deformity is evil" baggage that is already out there – especially since you are taking extra steps to say that "innocent babies" are slaughtered for the benefit of the population – that's not a eugenics metaphor, that's straight-up eugenics.

It's not clear from the question or comments how you are slanting this practice (justified in-world, or un-justified).

Drawing from real world situations

There are real world societies which have committed infanticide, sometimes through ideology but often out of survival/necessity (drought, famine). It's difficult to find non-polemic research since "baby-killing" is a moral extreme used to invoke an emotional impulse (revulsion, outrage).

If you choose to research real life situations, remember that in these societies there is no birth-control or social welfare. Babies "happen" about once a year, and survival of your existing children might require "cutting losses" with an infant that you know will prevent you working, or feeding the others.

This might be a way to bring readers around to the idea, acknowledging there is no other choice. It must be a very difficult decision for the parents, but they view it as protecting their other children (not just society in general, but the life-and-death of the siblings).

Dr. Xavier's School for Gifted Children

You'll still have readers wondering why the "mutants" can't just go to "Hogwarts" and be with others of their own kind where they learn to control their powers. You may need to provide an in-world explanation.

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Killing babies is taboo for us, but not for them

The easiest way to humanize something is to show why it's done. Explain, through expository, the physical and cultural circumstances that lead a character to kill an infant. This applies to infanticide, fratricide, genocide, regicide, and every other kind of -cide there is. While modern readers may be horrified by the result (perhaps this is the intent), if the expository is sufficiently persuasive, the reader should as least understand why the character takes that action even if the reader doesn't agree it 'the right thing to do'.

If the babies are being killed because of resource constraints, then describe in as vivid detail as possible those constraints. If they are killed because of cultural traditions/misunderstandings then describe that culture.

The fundamental problem in describing this is that modern first world societies can "afford" to pay the costs of physically/mentally disabled children and adults. There are much stronger limitations on what can be done to people in the out-group. Readers coming from modern societies just don't have a good handle on what really deep privation looks like, or the feelings of abject fear at the unfamiliar. It is difficult for them to relate to circumstances where killing a baby (directly or through inaction) is the 'right thing to do'.

Many human societies throughout history have practiced infanticide, for many different reasons. A quick reading through the Infanticide Wikipedia entries shows that it's a very old practice.

There is a fine line to walk on this topic. Advocating infanticide is different than describing it. The author will need to be very careful to describe the practice of infanticide and the reasoning of those who do it, without condoning that behavior.

You want the reader to say, "Oh, I get why you would do that. It's horrific in the extreme but I get why you do it."

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Infanticide has been a part of many cultures and children seen as deformed or unlikely to survive would be left to die of exposure. It was a fact of life that no one need like, but it was done as there was no real alternative. The series Vikings had an episode where Ragnar takes his crippled infant son out to leave him, but has second thoughts and brings him back.

The weak were rarely permitted to drain the resources of the family. In the scenario you describe, such tainted children could be seen as potential connections to a darker god and a danger to all.

In Zelanzny’s This Immortal, the protagonist was left to die because of the day on which he was born, which according to his culture made him dangerous. Not all infants left to die do as others sometimes encounter them and adopt them - Oedipus for example.

Show the parents fear of the infant and fear for the harsh life he or she would have if left to live. A potential threat to society and marginalized - essentially a leper. It could be seen as a desperate act of love - ‘Can’t let this sweet babe suffer, so goodbye and better luck next time’ and then the parent kills the child to prevent his future suffering.

The doctor or whoever examined the infant to determine if they are worthy of life can be shown to dislike this aspect of life, but understand that preventing pain is a good thing. Living on the margins, looking like some kind of demon, the child was damned from the start.

Statistics showing the propensity for such a child to go dark - because of ostracism - would be given and mention of some of the more dangerous among them whose parents had hidden them away rather than do the responsible thing. Society demands what it demands.

In China, under the one child rule, many daughters were left to die so the parents could have a son to pass on the family name. Such sons had difficulty finding wives as many hadn’t been allowed to live.

Life can be dark and almost anything can have a reason or rationalization. Make it necessary and the reader will accept it.

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You won't be able to portray it in a less negative way, unless you try to really force your hand on the "good vs evil" theme, and even then you would raise eyebrows.

You stated that those children are not born evil, so we are already on a different track.

First of all, consider that one of the common and (imho) best practices is to prioritize the wellbeing of the mother over the wellbeing of the newborn (opinions may differ, but we're not here to discuss this).
If those mutated newborns are a danger for the mother, you've got a problem before the actual birth. The best you can do in those cases is to read how/when termination of pregnancy is done in our society, and compare with how/when it could be done in your alternate setting.
Another thing you have to consider is the actual survival rate of the mutated children; are they generally lower or higher? Do those mutated humans experience severe lack of phisical skills, or chronic pain? Is there a way for the doctor to estimate it? It's relevant since at this stage it does weight on the decision.
You already mentioned runes, so I imagine they could be further applied to this delicate area.

After the babies are born, you'll have an harder time making their killing "sympathetic". While in another time the killing of newborn babies was somewhat a last resort practice in other eras (think about the classical "leaving a baby in the woods" when a family could not feed him), the more modern you'll go and the more the reader will confront your in-world ethics with ours.
Moreover, there will be always the risk of readers seeing an allegory where there is none, and that's a problem in itself.

What you can do is to show how the ethics in your society are different, and yet problematic. To do this well, you have to present different arguments and counter-arguments to the topic, without clearly parading from one of them.

The parents will bond with their child, no matter if it's deformed. They will suffer the decision of killing it, even if their society always taught them not to.
Some of the corrupted babies reach adulthood. Some are "evil". Some will likely campaign about how harder is for them to live at the margin of society.
Some humans will find the practice of killing babies barbaric, no matter what.
Some others will have strong hate (from xenophobic reasons to religious to personal) towards the corruption, and will defend even harsher measures against it.
Some of the corrupted babies will live a life in pain. Some will be able to live normally. Some will act "evil", some won't.

As a writer, you have the duty to present every side of the issue fairly, without parading for one or the other. You may be tempted to reach out to the reader and say: "Look, I know killing newborns is bad, but here they have reasons". The reader will understand why it happens in your setting if you show it, but they won't like be schooled or spoonfeeded about it.

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