What could possibly be in the vaccines that would be worse than your child no longer existing?
The article says the man is a Mennonite, which means he probably believes in an afterlife. In his mind his child still exists and he'll get to see her again when he passes and spends eternity there.
I pretty firmly believe that afterlife beliefs account for a pretty significant distortion of values in people and helps explain a large number of frankly insane behaviours. Preventing deaths becomes much less important when there's an eternal paradise waiting for you and the "real" risk is doing something that bars you from going there.
You stated the reason yourself. Those are different values and matching in a case-insensitive manner is more work under the hood.