I think everyone has moments where we think "if only _this-and-such bad thing_ would happen to this person, then _this-and-such good_ would come of it."
Whatever the reasons, we have to remind ourselves of a few things in that kind of situation. Firstly, it is always wrong to wish evil upon someone. Secondly, while we may think we're wishing good upon them, only God knows what suffering, what temptations, what possible destruction of soul that person would undergo if our evil wish actually came true. We may THINK no bad could come of it, but we do not know the person's mind, heart, soul, strength to adhere to the right path, or what have you. Only God knows a soul well enough to know what is REALLY best for them, or how REALLY to save their soul. Finally, we should remember that no matter how much we love that person, God loves them more. And only He knows how best to take care of that person to give them the best chance of saving their souls. And as for cases of wishing evil upon people in terms of punishment for some wrong done to us or others... God is merciful and patient, and desires to save souls, not hurt or condemn them. Do we resent His good because we have evil hearts? Do we think that our sense of justice is more perfect than His? We cannot think that. It is OBVIOUSLY wrong.
Ultimately, we have to trust that God knows best for that soul, and loves them far, far more than we do. We must realize that He both can and will give them the best circuмstances and guidance so that they have the opportunity to save their soul. But none of us can be exempt, for instance, from temptations, from sufferings, from the cruelty of people around us... None will be exempt from the sufferings of the Cross. If someone was tempted to wish, for instance, that their children all be born autistic or something, to the extent that they couldn't be culpable for their sins... well, that may sound well and good to us, but... WE wouldn't be the ones living the day-to-day hell that person would probably have to suffer being so unable to communicate with or connect with the world around them. Wishing them good in one way, by an EVIL wish, we unknowingly wish upon them countless unforeseen evils and sufferings, because unlike God, we do NOT know these things. We would spare that soul from one thing, only to inflict upon them countless others that perhaps would be the true loss of them, or truly too much for them to bear. God has given to each soul the life he or she SHOULD have, the life He wills them to have in His wisdom and providence. We cannot question that He knows what He is doing, or that He loves those souls, however bad their circuмstances seem to us. We have no idea how much worse it would be for them, if God gave them what WE think is best for them, instead of what He KNOWS is!
We should therefore always banish such temptations. However good they may seem, it is always wrong to wish evil on someone, and we do not know what a person would suffer, or what would REALLY happen with them, if that evil wish came true.
Just as it isn't the place of children to punish other children of the same family, no matter what their intentions, so, too, we must leave other souls and lives up to their heavenly Father, Who alone has the right, the authority, the knowledge, and the LOVE to do what is best and most merciful for that soul. To think otherwise, is to think that we know better than God, or that we are somehow kinder or more merciful. (Or in the case of wishing punishments or corrections upon people, that we are somehow wiser or more just.)
We have only to think of the implications of our evil thoughts toward God and His relation to souls, and even what it might mean for the souls themselves, that we are unaware of, and we can see immediately that such thoughts are absolutely wrong, and against charity and faith in God's abilities to care for souls.
It's always hard to see loved ones suffer, or anyone, for that matter (if we have the right love of souls in our hearts)... but he who does not take up the cross and follow God, is not worthy of Him.