Here’s how I see it.
Evil is the negation of the good. It isn’t a thing in itself. Natural evils are things like death, sickness, suffering. There is a loss of the good, but it’s not willful. It just happens. Moral evils are where we intentionally do evil through the use of our wills.
The Church teaches that the ends does not justify the means. As such, I would say that referring to worse evils that are prevented through things like war and capital punishment is actually arguing the reverse, that the ends sometimes does justify the means.
BUT, like divorce, God permits evil because of the hardness of our hearts. He allowed the law of Moses to include divorce, and He’s allowed the Church to permit evils like slavery and capital punishment.
But we are in an age where we are acknowledging the universal call to holiness gradually. This means we’re rejecting notions of marriage being some sort of moral concession to control our sexual appetite, as if lust were okay in marriage. It means that we acknowledge that abstinence in marriage may be prudent, that we can even speak of a grave moral reason to avoid pregnancy, meaning that sometimes it is gravely sinful to engage in sex with our spouses, even though we are married.
We are also acknowledging that the path to holiness is a gradual one. We must not become so obsessed with avoiding one type of sin that we engage in graver sins to avoid the lesser ones. THIS is a problem today.
So, yes, killing a human being (regardless of their guilt) is a moral evil. Their life is a gift from God. Is it an evil we’ve had to permit? Yes. Indeed, to not permit some moral evils do result in encouraging greater evils, but we need to acknowledge this. We need to grow in humility and stop thinking we’re holier than we are.