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.