Because, as I mentioned, it’s a magic thing. Is that plot armour? Yes indeed but it’s established continuity for decades that magic based attacks can hurt Kryptonians. But if you prefer to use that logic, why can’t a lion impregnate a housecat? They’re technically from the same species. See? Doesn’t work does it?
Then let’s take a moment to consider — in spite of the fact a child is in the womb, there is scientific evidence that shows that fetuses respond well to solar power. That means a part Kryptonian child, even while in the womb, will have their cells absorbing solar radiation. This means a Kryptonian pregnancy will most likely result in the death of the mother and maybe even the infant. A single super-powered baby kick could rupture the insides of a human woman, and cause her to die. The baby, in spite of its super powered origins, may not survive either.
In either case, Wonder Woman is strong enough to bare his children. So is Maxima