The solution to the problem of evil that you describe is called "skeptical theism" in the philosophy of religion literature. I think it has fatal problems. Let's suppose, like you say, that God permits all of the evils which seem to us to be gratuitous because God will bring a greater good out of them. That would mean that if you were confronted with a person suffering that you wouldn't be able to know whether you should help them or not. For all you know, this person's suffering is an instance of suffering for which God will bring out a greater good. So if you alleviate their suffering you could be thwarting God's plan and actually increasing the amount of evil in the world. You wouldn't know what to do in that situation although commonsense clearly says that you should help them. So skeptical theism leads to an abhorrent moral skepticism, a very high price to pay in order to solve the problem of evil. The problem of evil is the greatest obstacle to the acceptance of theism. If you really want to kill atheism, then I would suggest you post a lot more about it.
You can delete the above post. I meant to post it in the immaturity thread.