What justifications can a state provide its people that would rationalize this social policy? What methods can it use to reinforce it in society ?
This seems strange to you, I guess, because it's unthinkable in the modern era. But as other posters have pointed out, it's something that has precedent in the past.
It's actually stranger not to kill the deformed at birth culturally--at least in ancient history.
As to justification, you've already provided that more strongly than it's seen in the real world, by giving the deformities the ability to actually be a DANGER.
REAL WORLD JUSTIFICATION 1: Possible inability to work and a drain on resources.
In normal circumstances, killing deformed babies was common practice in ye olde times, because resources were scarcer and the ability to work was valued. A baby that merely had a club foot might be considered for euthanasia. Anything more serious could result in death for the child.
REAL WORLD STUMBLING BLOCK 1: Heir and a spare. Solution below.
That didn't mean that some deformed children were not allowed to live. But this depended often on social strata. For example, wealthier families might indulge, especially if they were desperate to produce an heir. It was always good to keep around a spare kid even if you'd already had some, just to pass things down, because disease could take them all. However, you could definitely help to make sure your nobles DON'T do this, by having some sort of inspection of their body before the crown/title is passed on when they are an adult. (Or have a certification done at birth.)
REAL WORLD JUSTIFICATION 2: Purity & pride. It's already been pointed out here that many societies, from the Spartans to the Nazis have used this as a reason.
REAL WORLD STUMBLING BLOCK 2: Hiding deformities. I know you said these deformities are obvious, but that doesn't have to be true and even so, in the real world people found lots of creative ways to hide deformities, if they could. In your world, you have the inspection at birth. Midwives would have to be above reproach, and the penalties for hiding that a child has a deformity might be death, or at the very least, social humiliation, and being stripped of their midwife license. If a kid has say, one scale--maybe that will fall off later? Or it could be removed by a discreet doctor?
I'd say there should be a certification that a kid gets at birth--a tiny defect like a small patch of scales and such might be watched, and they would not get certified pure, which means that they are not allowed to get married and have children. (Of course, this will result in common law marriages, and it will often be between the tainted, which may result in communities apart, which may occasionally be burned to the ground because the people there are blamed for whatever).
Whether a set up like this is allowed is going to depend on how many babies are born with some level of deformity. If you have a high birthrate, and a really low percentage of deformity, then killing them all, even if it's cosmetic and easily hidden, should be possible, if the consequences are dire.
And, if a child is discovered years later, what then? Because babies are cute, mothers love them, and there will be some, especially with minor defects that will not be killed, even if you kill any midwives that allow it. Should they be killed then? That's possible, but more difficult to do without eliciting sympathy, especially if they've been useful members of society. Depending on the frequency you have to do something with those--either give them a job that might kill them (fighting the creatures that have resulted from the Warp) or find another way to separate them from society.
Solutions here include 1) multiple witnesses at the birth 2) dire consequences for hiding such a thing 3) perhaps an inspection by several priests or priestesses prior to marriage to make sure you haven't been influenced by the Warp since your birth or as a second measure if perhaps your midwife allowed you to live.
REAL WORLD JUSTIFICATION 3: It's a hard knock life.
The easiest way to make it acceptable to kill babies, is to make sure that it's illustrated to people that the lives of the tainted are, in fact, more terrible than being alive. A mother would feel better about killing a child if, in fact they would be sparing them a life of misery and pain. In ye olden tymes, this was used as justification, but with your world, I am sure you can find a way to turn that up to 11. Government and society can participate in this. There should be caged carts with tainted people to illustrate this. Seriously.