Your options for this debate probably won't get much response, because people don't like to feel like we're trapped picking the lesser of two evils. In any case, the best Christian answer I've heard comes from CS Lewis in his Problem of Pain book. It's very complicated to boil down, but the main points I remember are:

God's love is like a father's love in that while you want to protect your children, they have to experience the world on their own and the suffering makes the good parts even better.

Much of the pain in the world comes from free will. If god prevented pain, then there would not be free will and consequences for actions.

Suffering in the world is nothing compared to the bliss of paradise. What we experience here is part of His plan and makes us choose Him or sin, so it's a test of free will.

Yes, he uses the convenient, woolly catchall of 'free will' often in his apologetics. The options I've offered in this debate are the only methods that conspicuously explain simultaneously maintained, mutually incompatible positions.

For example, if Jonny loves Jenny he's not likely to want harm to come to Jenny. If Jonny must harm Jenny in order to help her e.g. injection of some life saving substance, he can be said to 'harm' for a greater purpose. This seems to be CS Lewis' argument for all the horrors, injustices, accidents and consequences in the world.

This breaks down within the Christian context. A baby born to a God-fearing Christian family with massive, terminal physical deformities occurs because it is God's will in accordance with his omnipotence. The family maintain that God loves them and that the unfortunate child is a testament to that fact. So, allowing/willing a human to enter life compromised to the point of only living a few days/months/years, devastating the parents is a display of divine love. Suffering in this life is somehow compensated in the afterlife. In this life, it takes mental partitioning to get on with this idea.

Basically, think about things as if you were God. If you cured every illness, only allowed small amounts of pain to enter people's life, would people be more happy? Life would be too easy, people would start to complain about heartache and loneliness and why a benevolent god allows that. Maybe genetic defects are nature's way of exploring new avenues, so in the long run humanity will be better for it.

Nature or god puts our future and our present in our hands, and we can make of it whatever we want. I wouldn't have that robbed from me by not allowing bad things to happen. If every choice led to happiness, there really is no choice.

But he's not putting your life in your own hands if your hideously compromised with a congenital disease or stillborn for that matter.